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2wayvenn_text.R
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dhcp-7-243:~ messaoudilab3$ ssh arivera@pigeon.bioinfo.ucr.edu
arivera@pigeon.bioinfo.ucr.edu's password:
dhcp-7-243:~ messaoudilab3$ ssh ssure003@pigeon.bioinfo.ucr.edu
ssure003@pigeon.bioinfo.ucr.edu's password:
Last login: Fri Mar 9 15:57:51 2018 from 128.200.7.154
--------------------------------------------------------------------------------
University of California, Riverside - HPCC (High-Performance Computing Center)
--------------------------------------------------------------------------------
More information about HPCC and how to use the resources provided can
be found at http://hpcc.ucr.edu/manuals_linux-cluster_intro.html
Please send all questions and support requests to support@biocluster.ucr.edu
Note: The default version of R is now 3.4.2
--------------------------------------------------------------------------------
ssure003@pigeon:~$ cd bigdata/Projects/Maob_CD4_ATAC/
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_ATAC$ ll
total 1536
-rw-r--r-- 1 ssure003 messaoudilab 7406 Feb 26 15:47 Rplots.pdf
drwxr-xr-x 2 ssure003 messaoudilab 524288 Jan 28 19:26 alignment
-rw------- 1 ssure003 messaoudilab 395 Feb 9 15:20 atac_pipeline.sh.save
drwxr-xr-x 2 ssure003 messaoudilab 4096 Mar 1 18:27 edgeR
drwxr-xr-x 3 ssure003 messaoudilab 4096 Feb 1 17:22 peaks
drwxr-xr-x 2 ssure003 messaoudilab 4096 Feb 1 17:11 position_adjust
drwxr-xr-x 2 ssure003 messaoudilab 4096 Feb 1 17:10 post_alignment
-rw-r--r-- 1 ssure003 messaoudilab 1020 Feb 26 15:44 targets.txt
drwxr-xr-x 2 ssure003 messaoudilab 524288 Jan 24 17:39 trimmed_reads
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_ATAC$ R
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> q()
Save workspace image? [y/n/c]: n
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_ATAC$ ll
total 1536
-rw-r--r-- 1 ssure003 messaoudilab 7406 Feb 26 15:47 Rplots.pdf
drwxr-xr-x 2 ssure003 messaoudilab 524288 Jan 28 19:26 alignment
-rw------- 1 ssure003 messaoudilab 395 Feb 9 15:20 atac_pipeline.sh.save
drwxr-xr-x 2 ssure003 messaoudilab 4096 Mar 1 18:27 edgeR
drwxr-xr-x 3 ssure003 messaoudilab 4096 Feb 1 17:22 peaks
drwxr-xr-x 2 ssure003 messaoudilab 4096 Feb 1 17:11 position_adjust
drwxr-xr-x 2 ssure003 messaoudilab 4096 Feb 1 17:10 post_alignment
-rw-r--r-- 1 ssure003 messaoudilab 1020 Feb 26 15:44 targets.txt
drwxr-xr-x 2 ssure003 messaoudilab 524288 Jan 24 17:39 trimmed_reads
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_ATAC$ nano targets.txt
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_ATAC$ cd ..
ssure003@pigeon:~/bigdata/Projects$ ll
total 512
drwxr-xr-x 7 ssure003 messaoudilab 4096 Nov 19 12:09 ATAC_LPS_PUBLIC
drwxr-xr-x 5 ssure003 messaoudilab 4096 Nov 4 2015 Alcohol.lung
drwxr--r-- 15 ssure003 messaoudilab 4096 Nov 14 17:25 Alcohol_ATAC
drwxr-xr-x 5 ssure003 Users 4096 May 4 2016 Alcohol_PBMC
drwxr-xr-x 7 ssure003 messaoudilab 4096 Feb 22 16:11 Alcohol_PBMC_Stim
drwxr-xr-x 4 ssure003 messaoudilab 4096 Mar 6 17:53 Alcohol_PBMC_miRNA
drwxr-xr-x 9 ssure003 messaoudilab 4096 Nov 1 08:46 Alcohol_PBMC_new
drwxr-xr-x 12 ssure003 messaoudilab 4096 Aug 23 2017 Alcohol_Spleen_Stim
drwxr-xr-x 3 ssure003 Users 4096 May 5 2015 Alcohol_Vaccine_miRNA
drwxr-xr-x 2 ssure003 messaoudilab 4096 Jun 23 2017 Alcohol_colon
drwxr-xr-x 5 ssure003 messaoudilab 4096 Mar 14 2016 Alcohol_duodenum
drwxr-xr-x 6 ssure003 messaoudilab 4096 Oct 9 11:00 Alcohol_ileum
drwxr-xr-x 6 ssure003 Users 4096 Mar 14 2016 Alcohol_jejunum
drwxr-xr-x 5 ssure003 Users 4096 Nov 11 2015 Alcohol_paper
drwxr-xr-x 10 ssure003 messaoudilab 4096 Sep 8 2016 Alcohol_paper_new
drwxr-xr-x 4 ssure003 messaoudilab 4096 Nov 2 09:01 Alcohol_sex
drwxr-xr-x 6 ssure003 messaoudilab 4096 Sep 23 2015 Alcohol_vaccine
drwxr-xr-x 2 ssure003 messaoudilab 4096 Sep 7 2016 Androgen_luminex
drwxr-xr-x 2 ssure003 messaoudilab 4096 Feb 21 2017 CD103_tyler
drwxr-xr-x 2 ssure003 messaoudilab 4096 Nov 19 12:00 ChipSeq_LPS
drwxr-xr-x 7 ssure003 Users 4096 Jul 27 2015 EBOV-Thp1
drwxr-xr-x 8 ssure003 messaoudilab 4096 Jul 13 2016 HaIIa
drwxr-xr-x 7 ssure003 messaoudilab 4096 Mar 10 2017 Halla2
drwxr-xr-x 2 ssure003 messaoudilab 4096 Nov 22 2016 IsoGene
drwxr-xr-x 11 ssure003 messaoudilab 4096 Nov 19 22:30 MaOB_ATAC
drwxr-xr-x 9 ssure003 messaoudilab 4096 May 31 2017 MaOB_Stim_RNASeq
drwxr-xr-x 4 ssure003 messaoudilab 4096 Sep 19 12:18 MaOB_Tcell
drwxr-xr-x 2 ssure003 messaoudilab 4096 Feb 22 2017 MaOB_microbiome
drwxr-xr-x 11 ssure003 messaoudilab 4096 Sep 14 09:55 MaOb_placenta
drwxr-xr-x 2 ssure003 messaoudilab 4096 Jul 14 2017 MaoB_Integration
drwxr-xr-x 8 ssure003 messaoudilab 524288 Feb 26 14:45 Maob_CD4_ATAC
drwxr-xr-x 4 ssure003 messaoudilab 4096 Mar 9 10:53 Maob_CD4_RNAseq
drwxr-xr-x 4 ssure003 Users 4096 Jun 9 2015 Maob_lambda
drwxr-xr-x 2 ssure003 messaoudilab 4096 Dec 29 09:45 Maob_mom
drwxr-xr-x 12 ssure003 Users 4096 Feb 29 2016 Maob_new
drwxr-xr-x 15 ssure003 messaoudilab 4096 Aug 11 2017 Maternal_Obesity
drwxr-xr-x 4 ssure003 messaoudilab 4096 Oct 10 2016 Maternal_Obesity_RNASeq
drwxr-xr-x 3 ssure003 messaoudilab 4096 Jun 23 2017 MixOmics
drwxr-xr-x 12 ssure003 Users 4096 Mar 9 13:41 Moab
drwxr-xr-x 7 ssure003 messaoudilab 4096 Jan 4 2017 Nair
drwxr-xr-x 2 ssure003 Users 4096 May 4 2015 SVV-Lung
drwxr-xr-x 4 ssure003 Users 4096 May 18 2015 SVV-Skin
drwxr-xr-x 4 ssure003 messaoudilab 4096 May 10 2017 SVV_T-Cell
drwxr-xr-x 6 ssure003 Users 4096 Dec 3 2015 edmr
drwxr-xr-x 7 ssure003 Users 4096 Apr 27 2015 ganglia
drwxrwxrwx 4 ssure003 Users 4096 Feb 28 2016 gen242
ssure003@pigeon:~/bigdata/Projects$ cd Maob_CD4_RNAseq/
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ ll
total 512
-rw-r--r-- 1 ssure003 messaoudilab 5287 Mar 8 18:11 3D_CD4_Maob.pdf
-rw-r--r-- 1 ssure003 messaoudilab 3611 Mar 8 18:10 3D_leans.pdf
-rw-r--r-- 1 ssure003 messaoudilab 106 Mar 8 18:05 README.txt
-rw-r--r-- 1 ssure003 messaoudilab 0 Mar 8 18:20 Rplots.pdf
drwxr-xr-x 3 ssure003 messaoudilab 4096 Mar 9 13:22 data
drwxr-xr-x 20 ssure003 messaoudilab 4096 Mar 9 13:22 results
-rw-r--r-- 1 ssure003 messaoudilab 1844 Feb 16 15:26 slurm.tmpl
-rw-r--r-- 1 ssure003 messaoudilab 3183 Mar 9 11:13 targets.txt
-rw-r--r-- 1 ssure003 messaoudilab 1659 Mar 9 11:03 targets_CD4_new.txt
-rw-r--r-- 1 ssure003 messaoudilab 559 Feb 16 15:30 tophat.param
-rw-r--r-- 1 ssure003 messaoudilab 645 Feb 16 15:27 torque.tmpl
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ nano targets.txt
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ ibrary(systemPipeR)
-bash: syntax error near unexpected token `systemPipeR'
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ library(GenomicFeatures)
-bash: syntax error near unexpected token `GenomicFeatures'
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ #Read the targets file
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ targets <- read.delim("targets.txt", comment.char = "#")
-bash: syntax error near unexpected token `('
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ #Check if targets file is correct
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ targets
-bash: targets: command not found
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ #Create args
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ args <- systemArgs(sysma="tophat.param", mytargets="targets.txt")
-bash: syntax error near unexpected token `('
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ ll
total 512
-rw-r--r-- 1 ssure003 messaoudilab 5287 Mar 8 18:11 3D_CD4_Maob.pdf
-rw-r--r-- 1 ssure003 messaoudilab 3611 Mar 8 18:10 3D_leans.pdf
-rw-r--r-- 1 ssure003 messaoudilab 106 Mar 8 18:05 README.txt
-rw-r--r-- 1 ssure003 messaoudilab 0 Mar 8 18:20 Rplots.pdf
drwxr-xr-x 3 ssure003 messaoudilab 4096 Mar 9 13:22 data
drwxr-xr-x 20 ssure003 messaoudilab 4096 Mar 9 13:22 results
-rw-r--r-- 1 ssure003 messaoudilab 1844 Feb 16 15:26 slurm.tmpl
-rw-r--r-- 1 ssure003 messaoudilab 3198 Mar 9 16:33 targets.txt
-rw-r--r-- 1 ssure003 messaoudilab 1659 Mar 9 11:03 targets_CD4_new.txt
-rw-r--r-- 1 ssure003 messaoudilab 559 Feb 16 15:30 tophat.param
-rw-r--r-- 1 ssure003 messaoudilab 645 Feb 16 15:27 torque.tmpl
ssure003@pigeon:~/bigdata/Projects/Maob_CD4_RNAseq$ R
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> ibrary(systemPipeR)
Error in ibrary(systemPipeR) : could not find function "ibrary"
> library(GenomicFeatures)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
>
> #Read the targets file
> targets <- read.delim("targets.txt", comment.char = "#")
> #Check if targets file is correct
> targets
FileName1
1 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P01-ATTACTCG-TATAGCCT-Sequences.txt.gz_trimmed.fq.gz
2 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P02-GAATTCGT-TAATCTTA-Sequences.txt.gz_trimmed.fq.gz
3 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P03-GAGATTCC-GGCTCTGA-Sequences.txt.gz_trimmed.fq.gz
4 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P04-TAATGCGC-GTACTGAC-Sequences.txt.gz_trimmed.fq.gz
5 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P05-ATTCAGAA-AGGCGAAG-Sequences.txt.gz_trimmed.fq.gz
6 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P06-CTGAAGCT-CAGGACGT-Sequences.txt.gz_trimmed.fq.gz
7 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P07-TCCGGAGA-ATAGAGGC-Sequences.txt.gz_trimmed.fq.gz
8 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P08-CGCTCATT-CCTATCCT-Sequences.txt.gz_trimmed.fq.gz
SampleName Factor SampleLong Experiment Date
1 B005NS OBNS NA NA NA
2 B005S OBS NA NA NA
3 ME063NS LNNS NA NA NA
4 ME063S LNS NA NA NA
5 B015NS OBNS NA NA NA
6 B015S OBS NA NA NA
7 ME006NS LNNS NA NA NA
8 ME006S LNS NA NA NA
> #Create args
> args <- systemArgs(sysma="tophat.param", mytargets="targets.txt")
Error in systemArgs(sysma = "tophat.param", mytargets = "targets.txt") :
could not find function "systemArgs"
> moduleload(modules(args))
Error in moduleload(modules(args)) : could not find function "moduleload"
> library(systemPipeR)
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following object is masked from 'package:base':
apply
> args <- systemArgs(sysma="tophat.param", mytargets="targets.txt")
Warning messages:
1: In normalizePath(infile1) :
path[1]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P01-ATTACTCG-TATAGCCT-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
2: In normalizePath(infile1) :
path[2]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P02-GAATTCGT-TAATCTTA-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
3: In normalizePath(infile1) :
path[3]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P03-GAGATTCC-GGCTCTGA-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
4: In normalizePath(infile1) :
path[4]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P04-TAATGCGC-GTACTGAC-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
5: In normalizePath(infile1) :
path[5]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P05-ATTCAGAA-AGGCGAAG-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
6: In normalizePath(infile1) :
path[6]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P06-CTGAAGCT-CAGGACGT-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
7: In normalizePath(infile1) :
path[7]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P07-TCCGGAGA-ATAGAGGC-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
8: In normalizePath(infile1) :
path[8]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P08-CGCTCATT-CCTATCCT-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
> targets <- read.delim("targets.txt", comment.char = "#")
> targets
FileName1
1 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P01-ATTACTCG-TATAGCCT-Sequences.txt.gz_trimmed.fq.gz
2 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P02-GAATTCGT-TAATCTTA-Sequences.txt.gz_trimmed.fq.gz
3 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P03-GAGATTCC-GGCTCTGA-Sequences.txt.gz_trimmed.fq.gz
4 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P04-TAATGCGC-GTACTGAC-Sequences.txt.gz_trimmed.fq.gz
5 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P05-ATTCAGAA-AGGCGAAG-Sequences.txt.gz_trimmed.fq.gz
6 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P06-CTGAAGCT-CAGGACGT-Sequences.txt.gz_trimmed.fq.gz
7 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P07-TCCGGAGA-ATAGAGGC-Sequences.txt.gz_trimmed.fq.gz
8 /bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P08-CGCTCATT-CCTATCCT-Sequences.txt.gz_trimmed.fq.gz
SampleName Factor SampleLong Experiment Date
1 B005NS OBNS NA NA NA
2 B005S OBS NA NA NA
3 ME063NS LNNS NA NA NA
4 ME063S LNS NA NA NA
5 B015NS OBNS NA NA NA
6 B015S OBS NA NA NA
7 ME006NS LNNS NA NA NA
8 ME006S LNS NA NA NA
> args <- systemArgs(sysma="tophat.param", mytargets="targets.txt")
Warning messages:
1: In normalizePath(infile1) :
path[1]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P01-ATTACTCG-TATAGCCT-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
2: In normalizePath(infile1) :
path[2]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P02-GAATTCGT-TAATCTTA-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
3: In normalizePath(infile1) :
path[3]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P03-GAGATTCC-GGCTCTGA-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
4: In normalizePath(infile1) :
path[4]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P04-TAATGCGC-GTACTGAC-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
5: In normalizePath(infile1) :
path[5]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P05-ATTCAGAA-AGGCGAAG-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
6: In normalizePath(infile1) :
path[6]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P06-CTGAAGCT-CAGGACGT-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
7: In normalizePath(infile1) :
path[7]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P07-TCCGGAGA-ATAGAGGC-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
8: In normalizePath(infile1) :
path[8]="/bigdata/messaoudilab/ssure003/Projects/Maob_CD4_RNAseq/data/4R042-L3-P08-CGCTCATT-CCTATCCT-Sequences.txt.gz_trimmed.fq.gz": No such file or directory
> library(edgeR)
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
> countDF <- read.delim("results/countDFeByg.xls", row.names=1, check.names=FALSE)
> targets <- read.delim("targets.txt", comment="#")
> countDF2 <- subset(countDF, select = c(B005NS, B005S, ME063NS, ME063S, B015NS, B015S, ME006NS, ME006S))
> countDF3 <- subset(countDF2, rowMeans(countDF2) >= 5)
> edgeDF <- run_edgeR(countDF=countDF, targets=targets, cmp=cmp[[1]], independent=TRUE, mdsplot="")
Error in run_edgeR(countDF = countDF, targets = targets, cmp = cmp[[1]], :
object 'cmp' not found
> cmp <- readComp(file="targets.txt", format="matrix", delim="-")
> edgeDF <- run_edgeR(countDF=countDF3, targets=targets, cmp=cmp[[1]], independent=TRUE, mdsplot="")
Disp = 1.08183 , BCV = 1.0401
Disp = 0.50129 , BCV = 0.708
Disp = 1.00853 , BCV = 1.0043
> edgeDF <- cbind(edgeDF, desc[rownames(edgeDF),])
Error in desc[rownames(edgeDF), ] :
object of type 'closure' is not subsettable
> write.table(edgeDF, "./results/edgeRglm_allcomp.xls", quote=FALSE, sep="\t", col.names = NA)
>
> head(edgeDF)
OBS-OBNS_logFC OBS-OBNS_logCPM OBS-OBNS_LR OBS-OBNS_PValue
ENSG00000000003 -1.0728711 2.982615 0.31380196 0.5753565
ENSG00000000005 -1.0992647 3.146206 0.36381706 0.5463939
ENSG00000000419 0.2565602 3.458879 0.02372661 0.8775826
ENSG00000000457 -0.5418826 6.471826 0.14087525 0.7074124
ENSG00000000460 -0.5825893 7.346879 0.11242904 0.7373955
ENSG00000000938 -1.5586799 3.897271 0.71288870 0.3984865
OBS-OBNS_FDR LNS-LNNS_logFC LNS-LNNS_logCPM LNS-LNNS_LR
ENSG00000000003 0.9999594 5.9223879 2.970487 7.2354119
ENSG00000000005 0.9999594 5.2610316 2.559027 6.0572912
ENSG00000000419 0.9999594 -1.3057800 2.339204 0.4718022
ENSG00000000457 0.9999594 -0.9508233 5.780902 1.7682999
ENSG00000000460 0.9999594 -0.5957488 7.137969 0.8562013
ENSG00000000938 0.9999594 -0.8583241 3.056955 0.3250178
LNS-LNNS_PValue LNS-LNNS_FDR OBNS-LNNS_logFC OBNS-LNNS_logCPM
ENSG00000000003 0.007147941 0.1200157 5.6044663 2.560283
ENSG00000000005 0.013848995 0.1540277 5.8188842 2.684084
ENSG00000000419 0.492159256 0.8154139 0.8771520 2.909894
ENSG00000000457 0.183592621 0.5654637 0.2545419 6.304354
ENSG00000000460 0.354803919 0.7259074 -0.1098768 7.364166
ENSG00000000938 0.568607633 0.8543912 1.1380205 3.865601
OBNS-LNNS_LR OBNS-LNNS_PValue OBNS-LNNS_FDR
ENSG00000000003 3.811537744 0.05090070 0.9999637
ENSG00000000005 4.425395349 0.03540791 0.9999637
ENSG00000000419 0.181443188 0.67013591 0.9999637
ENSG00000000457 0.048699128 0.82534255 0.9999637
ENSG00000000460 0.006458457 0.93594734 0.9999637
ENSG00000000938 0.409062122 0.52244592 0.9999637
> pdf("results/DEGcounts.pdf")
> DEG_list <- filterDEGs(degDF=edgeDF, filter=c(Fold=2, FDR=5))
> dev.off()
null device
1
> DEG_list
$UporDown
$UporDown$`OBS-OBNS`
NULL
$UporDown$`LNS-LNNS`
[1] "ENSG00000002919" "ENSG00000004700" "ENSG00000005156" "ENSG00000009694"
[5] "ENSG00000013725" "ENSG00000033327" "ENSG00000044574" "ENSG00000053524"
[9] "ENSG00000057252" "ENSG00000069018" "ENSG00000075035" "ENSG00000076242"
[13] "ENSG00000083097" "ENSG00000087995" "ENSG00000089169" "ENSG00000095380"
[17] "ENSG00000100109" "ENSG00000100242" "ENSG00000100413" "ENSG00000101000"
[21] "ENSG00000101342" "ENSG00000102445" "ENSG00000103257" "ENSG00000103266"
[25] "ENSG00000103351" "ENSG00000104611" "ENSG00000104888" "ENSG00000105127"
[29] "ENSG00000105290" "ENSG00000105643" "ENSG00000105819" "ENSG00000105835"
[33] "ENSG00000106009" "ENSG00000106105" "ENSG00000106246" "ENSG00000106560"
[37] "ENSG00000106785" "ENSG00000107742" "ENSG00000107949" "ENSG00000109775"
[41] "ENSG00000110080" "ENSG00000112761" "ENSG00000113296" "ENSG00000113558"
[45] "ENSG00000113578" "ENSG00000113971" "ENSG00000114767" "ENSG00000115392"
[49] "ENSG00000115419" "ENSG00000115685" "ENSG00000116580" "ENSG00000116649"
[53] "ENSG00000116977" "ENSG00000120210" "ENSG00000120688" "ENSG00000120725"
[57] "ENSG00000121644" "ENSG00000121853" "ENSG00000122223" "ENSG00000122483"
[61] "ENSG00000123454" "ENSG00000124092" "ENSG00000124440" "ENSG00000125148"
[65] "ENSG00000126838" "ENSG00000127124" "ENSG00000128594" "ENSG00000128617"
[69] "ENSG00000128872" "ENSG00000129048" "ENSG00000129250" "ENSG00000129595"
[73] "ENSG00000130703" "ENSG00000131849" "ENSG00000132522" "ENSG00000132749"
[77] "ENSG00000133302" "ENSG00000133858" "ENSG00000134193" "ENSG00000134207"
[81] "ENSG00000134330" "ENSG00000135047" "ENSG00000136040" "ENSG00000136098"
[85] "ENSG00000137094" "ENSG00000137331" "ENSG00000137642" "ENSG00000137802"
[89] "ENSG00000138079" "ENSG00000138175" "ENSG00000138193" "ENSG00000138443"
[93] "ENSG00000138448" "ENSG00000139116" "ENSG00000139289" "ENSG00000139722"
[97] "ENSG00000140675" "ENSG00000140968" "ENSG00000141367" "ENSG00000141378"
[101] "ENSG00000141522" "ENSG00000141576" "ENSG00000142694" "ENSG00000143156"
[105] "ENSG00000143740" "ENSG00000143819" "ENSG00000143882" "ENSG00000143994"
[109] "ENSG00000144161" "ENSG00000145416" "ENSG00000148158" "ENSG00000148834"
[113] "ENSG00000149792" "ENSG00000151240" "ENSG00000152092" "ENSG00000153029"
[117] "ENSG00000153048" "ENSG00000153162" "ENSG00000154227" "ENSG00000154719"
[121] "ENSG00000154920" "ENSG00000156928" "ENSG00000157315" "ENSG00000157613"
[125] "ENSG00000157734" "ENSG00000158828" "ENSG00000159214" "ENSG00000159261"
[129] "ENSG00000160194" "ENSG00000160683" "ENSG00000162813" "ENSG00000162836"
[133] "ENSG00000162892" "ENSG00000164068" "ENSG00000164164" "ENSG00000164211"
[137] "ENSG00000164543" "ENSG00000164741" "ENSG00000164845" "ENSG00000165195"
[141] "ENSG00000166147" "ENSG00000166250" "ENSG00000166321" "ENSG00000166979"
[145] "ENSG00000167065" "ENSG00000168386" "ENSG00000168734" "ENSG00000169562"
[149] "ENSG00000169967" "ENSG00000170275" "ENSG00000170624" "ENSG00000170627"
[153] "ENSG00000170835" "ENSG00000171004" "ENSG00000171503" "ENSG00000171517"
[157] "ENSG00000171724" "ENSG00000171790" "ENSG00000171819" "ENSG00000172915"
[161] "ENSG00000173208" "ENSG00000173452" "ENSG00000173627" "ENSG00000173728"
[165] "ENSG00000174038" "ENSG00000175197" "ENSG00000175634" "ENSG00000175792"
[169] "ENSG00000175899" "ENSG00000176014" "ENSG00000176148" "ENSG00000176857"
[173] "ENSG00000178430" "ENSG00000178568" "ENSG00000179218" "ENSG00000179564"
[177] "ENSG00000179598" "ENSG00000179837" "ENSG00000179840" "ENSG00000180509"
[181] "ENSG00000181027" "ENSG00000182347" "ENSG00000182541" "ENSG00000182795"
[185] "ENSG00000183011" "ENSG00000183305" "ENSG00000183780" "ENSG00000184258"
[189] "ENSG00000184343" "ENSG00000184682" "ENSG00000184986" "ENSG00000185055"
[193] "ENSG00000185361" "ENSG00000187634" "ENSG00000188242" "ENSG00000188582"
[197] "ENSG00000188687" "ENSG00000189129" "ENSG00000196400" "ENSG00000196781"
[201] "ENSG00000196970" "ENSG00000197085" "ENSG00000197580" "ENSG00000197665"
[205] "ENSG00000197982" "ENSG00000198624" "ENSG00000198909" "ENSG00000199938"
[209] "ENSG00000202502" "ENSG00000203280" "ENSG00000204001" "ENSG00000204049"
[213] "ENSG00000204420" "ENSG00000205246" "ENSG00000205268" "ENSG00000205414"
[217] "ENSG00000205424" "ENSG00000205537" "ENSG00000205771" "ENSG00000205790"
[221] "ENSG00000211701" "ENSG00000212342" "ENSG00000213049" "ENSG00000213420"
[225] "ENSG00000213885" "ENSG00000213918" "ENSG00000214354" "ENSG00000214783"
[229] "ENSG00000214844" "ENSG00000214851" "ENSG00000216639" "ENSG00000218226"
[233] "ENSG00000220695" "ENSG00000222501" "ENSG00000223486" "ENSG00000223669"
[237] "ENSG00000224063" "ENSG00000224113" "ENSG00000224401" "ENSG00000224407"
[241] "ENSG00000224429" "ENSG00000224539" "ENSG00000224609" "ENSG00000224721"
[245] "ENSG00000224791" "ENSG00000225284" "ENSG00000225420" "ENSG00000225721"
[249] "ENSG00000226167" "ENSG00000226394" "ENSG00000226455" "ENSG00000226457"
[253] "ENSG00000226647" "ENSG00000226925" "ENSG00000226945" "ENSG00000227218"
[257] "ENSG00000227278" "ENSG00000227627" "ENSG00000227714" "ENSG00000227906"
[261] "ENSG00000228157" "ENSG00000228275" "ENSG00000228302" "ENSG00000228340"
[265] "ENSG00000228421" "ENSG00000228597" "ENSG00000228838" "ENSG00000228925"
[269] "ENSG00000229047" "ENSG00000229431" "ENSG00000229502" "ENSG00000229559"
[273] "ENSG00000229664" "ENSG00000229696" "ENSG00000229915" "ENSG00000230255"
[277] "ENSG00000230424" "ENSG00000230499" "ENSG00000230532" "ENSG00000230638"
[281] "ENSG00000230881" "ENSG00000230955" "ENSG00000230992" "ENSG00000231028"
[285] "ENSG00000231128" "ENSG00000231201" "ENSG00000231322" "ENSG00000231616"
[289] "ENSG00000231665" "ENSG00000231956" "ENSG00000231962" "ENSG00000231999"
[293] "ENSG00000232447" "ENSG00000232533" "ENSG00000232713" "ENSG00000232772"
[297] "ENSG00000232788" "ENSG00000232811" "ENSG00000232837" "ENSG00000232888"
[301] "ENSG00000233478" "ENSG00000233559" "ENSG00000234084" "ENSG00000234197"
[305] "ENSG00000234332" "ENSG00000234883" "ENSG00000235036" "ENSG00000235079"
[309] "ENSG00000235085" "ENSG00000235191" "ENSG00000235381" "ENSG00000235413"
[313] "ENSG00000236383" "ENSG00000236498" "ENSG00000236559" "ENSG00000236782"
[317] "ENSG00000236896" "ENSG00000237054" "ENSG00000237243" "ENSG00000237263"
[321] "ENSG00000237329" "ENSG00000237522" "ENSG00000237568" "ENSG00000237786"
[325] "ENSG00000237911" "ENSG00000238091" "ENSG00000238107" "ENSG00000238221"
[329] "ENSG00000238258" "ENSG00000238271" "ENSG00000238280" "ENSG00000238974"
[333] "ENSG00000240303" "ENSG00000240350" "ENSG00000240571" "ENSG00000240579"
[337] "ENSG00000240761" "ENSG00000241511" "ENSG00000241568" "ENSG00000242444"
[341] "ENSG00000243055" "ENSG00000243243" "ENSG00000244203" "ENSG00000244265"
[345] "ENSG00000244556" "ENSG00000244701" "ENSG00000244953" "ENSG00000245164"
[349] "ENSG00000245534" "ENSG00000246203" "ENSG00000246250" "ENSG00000247373"
[353] "ENSG00000248664" "ENSG00000248696" "ENSG00000248980" "ENSG00000249249"
[357] "ENSG00000249310" "ENSG00000249318" "ENSG00000249489" "ENSG00000249593"
[361] "ENSG00000250033" "ENSG00000250186" "ENSG00000250240" "ENSG00000250274"
[365] "ENSG00000250602" "ENSG00000250714" "ENSG00000250770" "ENSG00000250877"
[369] "ENSG00000251920" "ENSG00000252800" "ENSG00000253102" "ENSG00000253125"
[373] "ENSG00000253311" "ENSG00000253356" "ENSG00000253607" "ENSG00000253667"
[377] "ENSG00000254003" "ENSG00000254027" "ENSG00000254064" "ENSG00000254266"
[381] "ENSG00000254429" "ENSG00000254680" "ENSG00000254693" "ENSG00000254855"
[385] "ENSG00000255038" "ENSG00000255092" "ENSG00000255114" "ENSG00000255192"
[389] "ENSG00000255224" "ENSG00000255252" "ENSG00000255320" "ENSG00000255566"
[393] "ENSG00000255933" "ENSG00000255959" "ENSG00000256069" "ENSG00000256164"
[397] "ENSG00000256364" "ENSG00000256482" "ENSG00000256655" "ENSG00000256690"
[401] "ENSG00000256733" "ENSG00000256813" "ENSG00000256817" "ENSG00000257105"
[405] "ENSG00000257453" "ENSG00000257605" "ENSG00000257607" "ENSG00000257663"
[409] "ENSG00000257941" "ENSG00000258017" "ENSG00000258086" "ENSG00000258092"
[413] "ENSG00000258232" "ENSG00000258377" "ENSG00000258378" "ENSG00000258521"
[417] "ENSG00000258545" "ENSG00000258581" "ENSG00000258646" "ENSG00000258666"
[421] "ENSG00000258824" "ENSG00000258891" "ENSG00000259007" "ENSG00000259113"
[425] "ENSG00000259177" "ENSG00000259279" "ENSG00000259519" "ENSG00000259521"
[429] "ENSG00000259884" "ENSG00000259939" "ENSG00000259954" "ENSG00000259972"
[433] "ENSG00000260252" "ENSG00000260304" "ENSG00000260349" "ENSG00000260350"
[437] "ENSG00000260466" "ENSG00000260488" "ENSG00000260534" "ENSG00000260583"
[441] "ENSG00000261105" "ENSG00000261448" "ENSG00000261604" "ENSG00000261731"
[445] "ENSG00000261839" "ENSG00000262112" "ENSG00000262312" "ENSG00000262319"
[449] "ENSG00000262429" "ENSG00000262477" "ENSG00000262831" "ENSG00000263198"
[453] "ENSG00000263272" "ENSG00000263585" "ENSG00000263859" "ENSG00000264019"
[457] "ENSG00000264324" "ENSG00000264339" "ENSG00000264475" "ENSG00000264590"
[461] "ENSG00000264701" "ENSG00000264926" "ENSG00000265401" "ENSG00000265474"
[465] "ENSG00000265490" "ENSG00000265511" "ENSG00000265840" "ENSG00000266173"
[469] "ENSG00000266341" "ENSG00000266347" "ENSG00000266466" "ENSG00000266651"
[473] "ENSG00000266936" "ENSG00000266975" "ENSG00000266988" "ENSG00000267122"
[477] "ENSG00000267247" "ENSG00000267337" "ENSG00000267436" "ENSG00000267458"
[481] "ENSG00000267496" "ENSG00000267852" "ENSG00000268059" "ENSG00000268355"
[485] "ENSG00000268432" "ENSG00000268457" "ENSG00000268810" "ENSG00000268865"
[489] "ENSG00000268983" "ENSG00000269086" "ENSG00000269151" "ENSG00000269215"
[493] "ENSG00000269795" "ENSG00000269926" "ENSG00000269950" "ENSG00000270050"
[497] "ENSG00000270084" "ENSG00000270277" "ENSG00000270696" "ENSG00000270953"
[501] "ENSG00000271680" "ENSG00000271913" "ENSG00000271927" "ENSG00000272009"
[505] "ENSG00000272114" "ENSG00000272273" "ENSG00000272694" "ENSG00000273090"
[509] "ENSG00000273218" "ENSG00000273319" "ENSG00000273398" "ENSG00000273443"
[513] "ENSG00000273445"
$UporDown$`OBNS-LNNS`
NULL
$Up
$Up$`OBS-OBNS`
NULL
$Up$`LNS-LNNS`
[1] "ENSG00000002919" "ENSG00000005156" "ENSG00000009694" "ENSG00000033327"
[5] "ENSG00000057252" "ENSG00000069018" "ENSG00000075035" "ENSG00000087995"
[9] "ENSG00000089169" "ENSG00000095380" "ENSG00000101000" "ENSG00000101342"
[13] "ENSG00000102445" "ENSG00000103351" "ENSG00000104611" "ENSG00000104888"
[17] "ENSG00000105643" "ENSG00000106009" "ENSG00000106560" "ENSG00000107742"
[21] "ENSG00000110080" "ENSG00000113296" "ENSG00000113558" "ENSG00000114767"
[25] "ENSG00000115685" "ENSG00000120688" "ENSG00000121644" "ENSG00000121853"
[29] "ENSG00000122223" "ENSG00000123454" "ENSG00000124092" "ENSG00000124440"
[33] "ENSG00000126838" "ENSG00000128872" "ENSG00000129250" "ENSG00000130703"
[37] "ENSG00000132749" "ENSG00000134193" "ENSG00000134207" "ENSG00000135047"
[41] "ENSG00000136098" "ENSG00000137642" "ENSG00000137802" "ENSG00000138175"
[45] "ENSG00000138448" "ENSG00000139116" "ENSG00000139722" "ENSG00000141576"
[49] "ENSG00000143819" "ENSG00000144161" "ENSG00000148158" "ENSG00000151240"
[53] "ENSG00000152092" "ENSG00000153029" "ENSG00000154227" "ENSG00000157613"
[57] "ENSG00000159261" "ENSG00000160194" "ENSG00000160683" "ENSG00000162813"
[61] "ENSG00000162836" "ENSG00000162892" "ENSG00000164211" "ENSG00000164741"
[65] "ENSG00000165195" "ENSG00000166147" "ENSG00000166250" "ENSG00000166979"
[69] "ENSG00000168734" "ENSG00000169562" "ENSG00000169967" "ENSG00000170275"
[73] "ENSG00000170624" "ENSG00000170627" "ENSG00000170835" "ENSG00000171004"
[77] "ENSG00000171517" "ENSG00000171724" "ENSG00000172915" "ENSG00000173208"
[81] "ENSG00000173452" "ENSG00000175634" "ENSG00000175899" "ENSG00000178568"
[85] "ENSG00000179598" "ENSG00000179840" "ENSG00000180509" "ENSG00000182541"
[89] "ENSG00000182795" "ENSG00000183305" "ENSG00000183780" "ENSG00000184682"
[93] "ENSG00000188582" "ENSG00000189129" "ENSG00000196781" "ENSG00000196970"
[97] "ENSG00000197085" "ENSG00000197580" "ENSG00000197665" "ENSG00000198624"
[101] "ENSG00000198909" "ENSG00000203280" "ENSG00000204001" "ENSG00000204049"
[105] "ENSG00000204420" "ENSG00000205414" "ENSG00000211701" "ENSG00000213049"
[109] "ENSG00000213420" "ENSG00000214844" "ENSG00000214851" "ENSG00000223486"
[113] "ENSG00000223669" "ENSG00000224113" "ENSG00000224539" "ENSG00000224609"
[117] "ENSG00000224791" "ENSG00000226945" "ENSG00000227218" "ENSG00000227906"
[121] "ENSG00000228157" "ENSG00000228340" "ENSG00000228421" "ENSG00000228597"
[125] "ENSG00000229559" "ENSG00000230255" "ENSG00000230992" "ENSG00000231322"
[129] "ENSG00000231962" "ENSG00000232447" "ENSG00000232533" "ENSG00000232772"
[133] "ENSG00000232788" "ENSG00000232837" "ENSG00000233478" "ENSG00000234332"
[137] "ENSG00000238107" "ENSG00000240761" "ENSG00000241511" "ENSG00000242444"
[141] "ENSG00000245164" "ENSG00000245534" "ENSG00000249318" "ENSG00000249489"
[145] "ENSG00000250274" "ENSG00000253311" "ENSG00000254429" "ENSG00000255192"
[149] "ENSG00000255320" "ENSG00000256069" "ENSG00000256817" "ENSG00000257105"
[153] "ENSG00000257607" "ENSG00000258086" "ENSG00000258545" "ENSG00000259939"
[157] "ENSG00000260488" "ENSG00000260534" "ENSG00000261448" "ENSG00000262312"
[161] "ENSG00000262319" "ENSG00000264926" "ENSG00000266173" "ENSG00000266988"
[165] "ENSG00000267247" "ENSG00000267337" "ENSG00000267496" "ENSG00000267852"
[169] "ENSG00000269086" "ENSG00000269215" "ENSG00000270277" "ENSG00000271680"
[173] "ENSG00000272694"
$Up$`OBNS-LNNS`
NULL
$Down
$Down$`OBS-OBNS`
NULL
$Down$`LNS-LNNS`
[1] "ENSG00000004700" "ENSG00000013725" "ENSG00000044574" "ENSG00000053524"
[5] "ENSG00000076242" "ENSG00000083097" "ENSG00000100109" "ENSG00000100242"
[9] "ENSG00000100413" "ENSG00000103257" "ENSG00000103266" "ENSG00000105127"
[13] "ENSG00000105290" "ENSG00000105819" "ENSG00000105835" "ENSG00000106105"
[17] "ENSG00000106246" "ENSG00000106785" "ENSG00000107949" "ENSG00000109775"
[21] "ENSG00000112761" "ENSG00000113578" "ENSG00000113971" "ENSG00000115392"
[25] "ENSG00000115419" "ENSG00000116580" "ENSG00000116649" "ENSG00000116977"
[29] "ENSG00000120210" "ENSG00000120725" "ENSG00000122483" "ENSG00000125148"
[33] "ENSG00000127124" "ENSG00000128594" "ENSG00000128617" "ENSG00000129048"
[37] "ENSG00000129595" "ENSG00000131849" "ENSG00000132522" "ENSG00000133302"
[41] "ENSG00000133858" "ENSG00000134330" "ENSG00000136040" "ENSG00000137094"
[45] "ENSG00000137331" "ENSG00000138079" "ENSG00000138193" "ENSG00000138443"
[49] "ENSG00000139289" "ENSG00000140675" "ENSG00000140968" "ENSG00000141367"
[53] "ENSG00000141378" "ENSG00000141522" "ENSG00000142694" "ENSG00000143156"
[57] "ENSG00000143740" "ENSG00000143882" "ENSG00000143994" "ENSG00000145416"
[61] "ENSG00000148834" "ENSG00000149792" "ENSG00000153048" "ENSG00000153162"
[65] "ENSG00000154719" "ENSG00000154920" "ENSG00000156928" "ENSG00000157315"
[69] "ENSG00000157734" "ENSG00000158828" "ENSG00000159214" "ENSG00000164068"
[73] "ENSG00000164164" "ENSG00000164543" "ENSG00000164845" "ENSG00000166321"
[77] "ENSG00000167065" "ENSG00000168386" "ENSG00000171503" "ENSG00000171790"
[81] "ENSG00000171819" "ENSG00000173627" "ENSG00000173728" "ENSG00000174038"
[85] "ENSG00000175197" "ENSG00000175792" "ENSG00000176014" "ENSG00000176148"
[89] "ENSG00000176857" "ENSG00000178430" "ENSG00000179218" "ENSG00000179564"
[93] "ENSG00000179837" "ENSG00000181027" "ENSG00000182347" "ENSG00000183011"
[97] "ENSG00000184258" "ENSG00000184343" "ENSG00000184986" "ENSG00000185055"
[101] "ENSG00000185361" "ENSG00000187634" "ENSG00000188242" "ENSG00000188687"
[105] "ENSG00000196400" "ENSG00000197982" "ENSG00000199938" "ENSG00000202502"
[109] "ENSG00000205246" "ENSG00000205268" "ENSG00000205424" "ENSG00000205537"
[113] "ENSG00000205771" "ENSG00000205790" "ENSG00000212342" "ENSG00000213885"
[117] "ENSG00000213918" "ENSG00000214354" "ENSG00000214783" "ENSG00000216639"
[121] "ENSG00000218226" "ENSG00000220695" "ENSG00000222501" "ENSG00000224063"
[125] "ENSG00000224401" "ENSG00000224407" "ENSG00000224429" "ENSG00000224721"
[129] "ENSG00000225284" "ENSG00000225420" "ENSG00000225721" "ENSG00000226167"
[133] "ENSG00000226394" "ENSG00000226455" "ENSG00000226457" "ENSG00000226647"
[137] "ENSG00000226925" "ENSG00000227278" "ENSG00000227627" "ENSG00000227714"
[141] "ENSG00000228275" "ENSG00000228302" "ENSG00000228838" "ENSG00000228925"
[145] "ENSG00000229047" "ENSG00000229431" "ENSG00000229502" "ENSG00000229664"
[149] "ENSG00000229696" "ENSG00000229915" "ENSG00000230424" "ENSG00000230499"
[153] "ENSG00000230532" "ENSG00000230638" "ENSG00000230881" "ENSG00000230955"
[157] "ENSG00000231028" "ENSG00000231128" "ENSG00000231201" "ENSG00000231616"
[161] "ENSG00000231665" "ENSG00000231956" "ENSG00000231999" "ENSG00000232713"
[165] "ENSG00000232811" "ENSG00000232888" "ENSG00000233559" "ENSG00000234084"
[169] "ENSG00000234197" "ENSG00000234883" "ENSG00000235036" "ENSG00000235079"
[173] "ENSG00000235085" "ENSG00000235191" "ENSG00000235381" "ENSG00000235413"
[177] "ENSG00000236383" "ENSG00000236498" "ENSG00000236559" "ENSG00000236782"
[181] "ENSG00000236896" "ENSG00000237054" "ENSG00000237243" "ENSG00000237263"
[185] "ENSG00000237329" "ENSG00000237522" "ENSG00000237568" "ENSG00000237786"
[189] "ENSG00000237911" "ENSG00000238091" "ENSG00000238221" "ENSG00000238258"
[193] "ENSG00000238271" "ENSG00000238280" "ENSG00000238974" "ENSG00000240303"
[197] "ENSG00000240350" "ENSG00000240571" "ENSG00000240579" "ENSG00000241568"
[201] "ENSG00000243055" "ENSG00000243243" "ENSG00000244203" "ENSG00000244265"
[205] "ENSG00000244556" "ENSG00000244701" "ENSG00000244953" "ENSG00000246203"
[209] "ENSG00000246250" "ENSG00000247373" "ENSG00000248664" "ENSG00000248696"
[213] "ENSG00000248980" "ENSG00000249249" "ENSG00000249310" "ENSG00000249593"
[217] "ENSG00000250033" "ENSG00000250186" "ENSG00000250240" "ENSG00000250602"
[221] "ENSG00000250714" "ENSG00000250770" "ENSG00000250877" "ENSG00000251920"
[225] "ENSG00000252800" "ENSG00000253102" "ENSG00000253125" "ENSG00000253356"
[229] "ENSG00000253607" "ENSG00000253667" "ENSG00000254003" "ENSG00000254027"
[233] "ENSG00000254064" "ENSG00000254266" "ENSG00000254680" "ENSG00000254693"
[237] "ENSG00000254855" "ENSG00000255038" "ENSG00000255092" "ENSG00000255114"
[241] "ENSG00000255224" "ENSG00000255252" "ENSG00000255566" "ENSG00000255933"
[245] "ENSG00000255959" "ENSG00000256164" "ENSG00000256364" "ENSG00000256482"
[249] "ENSG00000256655" "ENSG00000256690" "ENSG00000256733" "ENSG00000256813"
[253] "ENSG00000257453" "ENSG00000257605" "ENSG00000257663" "ENSG00000257941"
[257] "ENSG00000258017" "ENSG00000258092" "ENSG00000258232" "ENSG00000258377"
[261] "ENSG00000258378" "ENSG00000258521" "ENSG00000258581" "ENSG00000258646"
[265] "ENSG00000258666" "ENSG00000258824" "ENSG00000258891" "ENSG00000259007"
[269] "ENSG00000259113" "ENSG00000259177" "ENSG00000259279" "ENSG00000259519"
[273] "ENSG00000259521" "ENSG00000259884" "ENSG00000259954" "ENSG00000259972"
[277] "ENSG00000260252" "ENSG00000260304" "ENSG00000260349" "ENSG00000260350"
[281] "ENSG00000260466" "ENSG00000260583" "ENSG00000261105" "ENSG00000261604"
[285] "ENSG00000261731" "ENSG00000261839" "ENSG00000262112" "ENSG00000262429"
[289] "ENSG00000262477" "ENSG00000262831" "ENSG00000263198" "ENSG00000263272"
[293] "ENSG00000263585" "ENSG00000263859" "ENSG00000264019" "ENSG00000264324"
[297] "ENSG00000264339" "ENSG00000264475" "ENSG00000264590" "ENSG00000264701"
[301] "ENSG00000265401" "ENSG00000265474" "ENSG00000265490" "ENSG00000265511"
[305] "ENSG00000265840" "ENSG00000266341" "ENSG00000266347" "ENSG00000266466"
[309] "ENSG00000266651" "ENSG00000266936" "ENSG00000266975" "ENSG00000267122"
[313] "ENSG00000267436" "ENSG00000267458" "ENSG00000268059" "ENSG00000268355"
[317] "ENSG00000268432" "ENSG00000268457" "ENSG00000268810" "ENSG00000268865"
[321] "ENSG00000268983" "ENSG00000269151" "ENSG00000269795" "ENSG00000269926"
[325] "ENSG00000269950" "ENSG00000270050" "ENSG00000270084" "ENSG00000270696"
[329] "ENSG00000270953" "ENSG00000271913" "ENSG00000271927" "ENSG00000272009"
[333] "ENSG00000272114" "ENSG00000272273" "ENSG00000273090" "ENSG00000273218"
[337] "ENSG00000273319" "ENSG00000273398" "ENSG00000273443" "ENSG00000273445"
$Down$`OBNS-LNNS`
NULL
$Summary
Comparisons Counts_Up_or_Down Counts_Up Counts_Down
OBS-OBNS OBS-OBNS 0 0 0
LNS-LNNS LNS-LNNS 513 173 340
OBNS-LNNS OBNS-LNNS 0 0 0
> rpkmDFeByg <- read.delim("./results/rpkmDFeByg.xls", row.names=1, check.names=FALSE)[,-19]
> head(rpkmDFeByg)
B005NS B005S ME063NS ME063S B015NS B015S
ENSG00000000003 5.530106 1.644401 0.000000 5.6166270 0.4426049 0.8034866
ENSG00000000005 9.658070 4.850268 0.000000 4.8319272 2.4477975 0.7406050
ENSG00000000419 7.157090 15.365544 0.000000 0.0000000 5.4418034 1.9757648
ENSG00000000457 7.161149 8.801515 8.730066 5.0104190 17.1943892 10.0578381
ENSG00000000460 12.915765 13.365144 24.772833 15.2166924 35.7667108 22.5188678
ENSG00000000938 13.179222 3.652710 1.535929 0.3199031 0.0000000 0.3432280
ME006NS ME006S B009NS B009S B010S B010NS
ENSG00000000003 0.000000 2.043919 4.6312808 5.2307094 5.274873 6.756391
ENSG00000000005 0.000000 3.767920 0.7114721 0.5672176 13.775827 6.227630
ENSG00000000419 4.532284 2.512987 13.2863146 7.5660342 7.566332 9.493653
ENSG00000000457 7.955886 6.396312 10.9949139 11.9531456 4.553759 6.457679
ENSG00000000460 19.156105 22.436141 18.9289208 19.1152508 21.764731 18.259482
ENSG00000000938 1.968360 2.182769 2.9675392 1.8401100 3.755475 6.184607
ME001S ME027NS ME027S
ENSG00000000003 0.000000 4.147426 0.000000
ENSG00000000005 0.000000 16.140901 0.000000
ENSG00000000419 0.000000 2.266328 15.000579
ENSG00000000457 0.000000 6.166317 6.076553
ENSG00000000460 6.474741 17.650893 39.016178
ENSG00000000938 0.000000 3.149635 0.000000
> rpkm2 <- subset(rpkmDFeByg, select = c(B005NS, B005S, ME063NS, ME063S, B015NS, B015S, ME006NS, ME006S))
> head(rpkm2)
B005NS B005S ME063NS ME063S B015NS B015S
ENSG00000000003 5.530106 1.644401 0.000000 5.6166270 0.4426049 0.8034866
ENSG00000000005 9.658070 4.850268 0.000000 4.8319272 2.4477975 0.7406050
ENSG00000000419 7.157090 15.365544 0.000000 0.0000000 5.4418034 1.9757648
ENSG00000000457 7.161149 8.801515 8.730066 5.0104190 17.1943892 10.0578381
ENSG00000000460 12.915765 13.365144 24.772833 15.2166924 35.7667108 22.5188678
ENSG00000000938 13.179222 3.652710 1.535929 0.3199031 0.0000000 0.3432280
ME006NS ME006S
ENSG00000000003 0.000000 2.043919
ENSG00000000005 0.000000 3.767920
ENSG00000000419 4.532284 2.512987
ENSG00000000457 7.955886 6.396312
ENSG00000000460 19.156105 22.436141
ENSG00000000938 1.968360 2.182769
> rpkmDFeByg <- read.delim("./results/rpkmDFeByg.xls", check.names=FALSE)[,-19]
^[[A^[[A
> head(rpkm2)
B005NS B005S ME063NS ME063S B015NS B015S
ENSG00000000003 5.530106 1.644401 0.000000 5.6166270 0.4426049 0.8034866
ENSG00000000005 9.658070 4.850268 0.000000 4.8319272 2.4477975 0.7406050
ENSG00000000419 7.157090 15.365544 0.000000 0.0000000 5.4418034 1.9757648
ENSG00000000457 7.161149 8.801515 8.730066 5.0104190 17.1943892 10.0578381
ENSG00000000460 12.915765 13.365144 24.772833 15.2166924 35.7667108 22.5188678
ENSG00000000938 13.179222 3.652710 1.535929 0.3199031 0.0000000 0.3432280
ME006NS ME006S
ENSG00000000003 0.000000 2.043919
ENSG00000000005 0.000000 3.767920
ENSG00000000419 4.532284 2.512987
ENSG00000000457 7.955886 6.396312
ENSG00000000460 19.156105 22.436141
ENSG00000000938 1.968360 2.182769
>
>
>
> head(rpkmDFeByg)
B005NS B005S ME063NS ME063S B015NS
1 ENSG00000000003 5.530106 1.644401 0.000000 5.6166270 0.4426049
2 ENSG00000000005 9.658070 4.850268 0.000000 4.8319272 2.4477975
3 ENSG00000000419 7.157090 15.365544 0.000000 0.0000000 5.4418034
4 ENSG00000000457 7.161149 8.801515 8.730066 5.0104190 17.1943892
5 ENSG00000000460 12.915765 13.365144 24.772833 15.2166924 35.7667108
6 ENSG00000000938 13.179222 3.652710 1.535929 0.3199031 0.0000000
B015S ME006NS ME006S B009NS B009S B010S B010NS
1 0.8034866 0.000000 2.043919 4.6312808 5.2307094 5.274873 6.756391
2 0.7406050 0.000000 3.767920 0.7114721 0.5672176 13.775827 6.227630
3 1.9757648 4.532284 2.512987 13.2863146 7.5660342 7.566332 9.493653
4 10.0578381 7.955886 6.396312 10.9949139 11.9531456 4.553759 6.457679
5 22.5188678 19.156105 22.436141 18.9289208 19.1152508 21.764731 18.259482
6 0.3432280 1.968360 2.182769 2.9675392 1.8401100 3.755475 6.184607
ME001S ME027NS ME027S
1 0.000000 4.147426 0.000000
2 0.000000 16.140901 0.000000
3 0.000000 2.266328 15.000579
4 0.000000 6.166317 6.076553
5 6.474741 17.650893 39.016178
6 0.000000 3.149635 0.000000
> rpkm2 <- subset(rpkmDFeByg, select = c(B005NS, B005S, ME063NS, ME063S, B015NS, B015S, ME006NS, ME006S))
> head(edgeDF)
OBS-OBNS_logFC OBS-OBNS_logCPM OBS-OBNS_LR OBS-OBNS_PValue
ENSG00000000003 -1.0728711 2.982615 0.31380196 0.5753565
ENSG00000000005 -1.0992647 3.146206 0.36381706 0.5463939
ENSG00000000419 0.2565602 3.458879 0.02372661 0.8775826
ENSG00000000457 -0.5418826 6.471826 0.14087525 0.7074124
ENSG00000000460 -0.5825893 7.346879 0.11242904 0.7373955
ENSG00000000938 -1.5586799 3.897271 0.71288870 0.3984865
OBS-OBNS_FDR LNS-LNNS_logFC LNS-LNNS_logCPM LNS-LNNS_LR
ENSG00000000003 0.9999594 5.9223879 2.970487 7.2354119
ENSG00000000005 0.9999594 5.2610316 2.559027 6.0572912
ENSG00000000419 0.9999594 -1.3057800 2.339204 0.4718022
ENSG00000000457 0.9999594 -0.9508233 5.780902 1.7682999
ENSG00000000460 0.9999594 -0.5957488 7.137969 0.8562013
ENSG00000000938 0.9999594 -0.8583241 3.056955 0.3250178
LNS-LNNS_PValue LNS-LNNS_FDR OBNS-LNNS_logFC OBNS-LNNS_logCPM
ENSG00000000003 0.007147941 0.1200157 5.6044663 2.560283
ENSG00000000005 0.013848995 0.1540277 5.8188842 2.684084
ENSG00000000419 0.492159256 0.8154139 0.8771520 2.909894
ENSG00000000457 0.183592621 0.5654637 0.2545419 6.304354
ENSG00000000460 0.354803919 0.7259074 -0.1098768 7.364166
ENSG00000000938 0.568607633 0.8543912 1.1380205 3.865601
OBNS-LNNS_LR OBNS-LNNS_PValue OBNS-LNNS_FDR
ENSG00000000003 3.811537744 0.05090070 0.9999637
ENSG00000000005 4.425395349 0.03540791 0.9999637
ENSG00000000419 0.181443188 0.67013591 0.9999637
ENSG00000000457 0.048699128 0.82534255 0.9999637
ENSG00000000460 0.006458457 0.93594734 0.9999637
ENSG00000000938 0.409062122 0.52244592 0.9999637
> merge <- merge(edgeDF, rpkm2, by.x="V1", by.y="V1")
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
> merge <- merge(edgeDF, rpkm2, by.x=c(1), by.y=c(1))
> head(merge)
[1] OBS-OBNS_logFC OBS-OBNS_logCPM OBS-OBNS_LR OBS-OBNS_PValue
[5] OBS-OBNS_FDR LNS-LNNS_logFC LNS-LNNS_logCPM LNS-LNNS_LR
[9] LNS-LNNS_PValue LNS-LNNS_FDR OBNS-LNNS_logFC OBNS-LNNS_logCPM
[13] OBNS-LNNS_LR OBNS-LNNS_PValue OBNS-LNNS_FDR B005S
[17] ME063NS ME063S B015NS B015S
[21] ME006NS ME006S
<0 rows> (or 0-length row.names)
> merge <- merge(edgeDF, rpkm2, by.x=c(,1), by.y=c(,1))
Error in c(, 1) : argument 1 is empty
> packet_write_wait: Connection to 138.23.51.90 port 22: Broken pipe
dhcp-7-243:~ messaoudilab3$ ssh arivera@pigeon.bioinfo.ucr.edu
arivera@pigeon.bioinfo.ucr.edu's password:
Last login: Sat Apr 7 15:54:44 2018 from 68.5.102.35
--------------------------------------------------------------------------------
University of California, Riverside - HPCC (High-Performance Computing Center)
--------------------------------------------------------------------------------
More information about HPCC and how to use the resources provided can
be found at http://hpcc.ucr.edu/manuals_linux-cluster_intro.html
Please send all questions and support requests to support@biocluster.ucr.edu
Note: The default version of R is now 3.4.2
--------------------------------------------------------------------------------
vim(3):ERROR:105: Unable to locate a modulefile for 'vim/7.3'
tmux(3):ERROR:105: Unable to locate a modulefile for 'tmux/1.6'
arivera@pigeon:~$ ls
R arivera cnguy087 fengelmann imessaoudi narnold ncbi rwilson ssure003 suhas_temp tbarr
arivera@pigeon:~$ cd arivera/Scripts/
arivera@pigeon:~/arivera/Scripts$ nano heatmap_v1_rev.R
arivera@pigeon:~/arivera/Scripts$ cd
arivera@pigeon:~$ ls
R arivera cnguy087 fengelmann imessaoudi narnold ncbi rwilson ssure003 suhas_temp tbarr
arivera@pigeon:~$ cd arivera/
arivera@pigeon:~/arivera$ ls
2.5.3a.tar.gz Androgen EBOV GEN242 Human_Placenta MARV RNA-Seq.R Rprogramming SVV YFV sequences viral_genomes
Aging_RO1 CHIKV GEN220 HG38 Jejunum MARV_U19 Reference_Macaque STAR-2.5.3a Scripts download subread-1.6.0-source
arivera@pigeon:~/arivera$ cd EBOV/rVSV_innate/
.BatchJobs.R data/ oldtargetfiles/ sequences/ targets_d-14.txt targets_d-3_NS.txt tophat.param
Cross_sect_Baseline/ extraction/ results/ targets-d-21.txt targets_d-28.txt targets_d-3_S.txt torque.tmpl
d-3_group_newanalysis/ heatmap/ scatter/ targets_alld0s.txt targets_d-3.txt targets_d-7.txt venn/
arivera@pigeon:~/arivera$ cd EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap$ ls
common_down.txt common_up.txt d-3_d14_d28_enrichment_list.txt d28_immunesystemprocess.txt nonviremic_heatmap.pdf viremic_down.txt viremic_up.txt
common_down_heatmap.pdf common_up_heatmap.pdf d-3_master.xls d28_immunesystemprocess_heatmap.pdf nonviremic_list.txt viremic_down_heatmap.pdf viremic_up_heatmap.pdf
common_heatmap.pdf d-3_d14_d28_enrichment_FDR.txt d14_immunesystemprocess.txt nonviremic_down.txt nonviremic_up.txt viremic_heatmap.pdf
common_list.txt d-3_d14_d28_enrichment_heatmap.pdf d14_immunesystemprocess_heatmap.pdf nonviremic_down_heatmap.pdf nonviremic_up_heatmap.pdf viremic_list.txt
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap$ ls -al
total 10240
drwxr-xr-x 2 arivera messaoudilab 4096 Apr 8 17:53 .
drwxr-xr-x 5 arivera messaoudilab 4096 Apr 7 11:33 ..
-rw-r--r-- 1 arivera messaoudilab 78 Apr 7 12:13 common_down.txt
-rw-r--r-- 1 arivera messaoudilab 5517 Apr 7 12:38 common_down_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 6808 Apr 8 15:42 common_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 241 Apr 8 15:09 common_list.txt
-rw-r--r-- 1 arivera messaoudilab 327 Apr 7 12:03 common_up.txt
-rw-r--r-- 1 arivera messaoudilab 7598 Apr 7 12:38 common_up_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 483 Apr 8 17:13 d-3_d14_d28_enrichment_FDR.txt
-rw-r--r-- 1 arivera messaoudilab 5064 Apr 8 17:14 d-3_d14_d28_enrichment_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 276 Apr 8 17:13 d-3_d14_d28_enrichment_list.txt
-rw-r--r-- 1 arivera messaoudilab 3908038 Apr 8 15:39 d-3_master.xls
-rw-r--r-- 1 arivera messaoudilab 253 Apr 8 17:55 d14_immunesystemprocess.txt
-rw-r--r-- 1 arivera messaoudilab 6541 Apr 8 17:55 d14_immunesystemprocess_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 272 Apr 8 17:49 d28_immunesystemprocess.txt
-rw-r--r-- 1 arivera messaoudilab 6665 Apr 8 17:53 d28_immunesystemprocess_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 92 Apr 7 12:14 nonviremic_down.txt
-rw-r--r-- 1 arivera messaoudilab 5429 Apr 7 12:41 nonviremic_down_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 6565 Apr 8 15:47 nonviremic_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 248 Apr 8 15:31 nonviremic_list.txt
-rw-r--r-- 1 arivera messaoudilab 198 Apr 7 12:10 nonviremic_up.txt
-rw-r--r-- 1 arivera messaoudilab 6475 Apr 7 12:40 nonviremic_up_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 158 Apr 7 12:11 viremic_down.txt
-rw-r--r-- 1 arivera messaoudilab 6121 Apr 7 12:35 viremic_down_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 6503 Apr 8 15:45 viremic_heatmap.pdf
-rw-r--r-- 1 arivera messaoudilab 236 Apr 8 15:45 viremic_list.txt
-rw-r--r-- 1 arivera messaoudilab 111 Apr 7 12:04 viremic_up.txt
-rw-r--r-- 1 arivera messaoudilab 5581 Apr 7 12:33 viremic_up_heatmap.pdf
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap$ mkdir test
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap$ mv common_list.txt test/
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap$ mv d-3_master.xls test/
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap$ cd test/
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ ls
common_list.txt d-3_master.xls
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ nano common_list.txt
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ nano d-3_master.xls
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ nano blank
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ ls
common_list.txt d-3_master.xls
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ nano d-3_master.xls
arivera@pigeon:~/arivera/EBOV/rVSV_innate/d-3_group_newanalysis/heatmap/test$ Rscript /bigdata/messaoudilab/arivera/Scripts/heatmap_v1_rev.R common_list.txt d-3_master.xls common
Loading required package: grid
Loading required package: futile.logger
V1 d28_183_d0 d28_184_d0 BL X195_d0 X195_d3
1 AIM2 345.7429143 448.1795626 396.9612385 1049.8732820 1192.7796360
2 CD177 2.4769751 24.8880751 13.6825251 3.6828516 105.6847078
3 CD274 18.3505396 13.1520762 15.7513079 65.3394457 112.6840097
4 CXCL10 2.7322359 3.3390330 3.0356345 14.3112676 17.8865391
5 FAS 19.4355986 13.8130523 16.6243255 25.8400220 98.4982567
6 FCER1G 23.7899015 39.2712423 31.5305719 55.6281151 122.8480314
7 FCN1 29.0167952 84.2425662 56.6296807 63.7550108 209.8070618
8 GBP3 10.5220007 3.9819385 7.2519696 38.2941589 106.3635122
9 GCH1 1.9208743 1.2046267 1.5627505 9.8000747 21.4723594
10 HERC5 10.9550351 10.0114189 10.4832270 56.5530538 212.6935685
11 ICAM1 1.0773730 1.4741381 1.2757556 1.7029561 1.9743576
12 IFI35 33.5945183 15.8728935 24.7337059 39.5971157 239.8205371
13 IFIH1 32.0695991 17.8826087 24.9761039 63.7899418 183.1913396
14 IFIT1 87.1578632 105.8195179 96.4886906 445.9882354 1544.5600520
15 IFITM1 217.7837784 82.4946182 150.1391983 326.0858178 1398.2329180
16 IL18 5.4676825 0.0000000 2.7338412 5.5361785 0.0000000
17 IL1RN 12.8305697 1.3504381 7.0905039 11.2217242 58.2882094
18 IRAK2 2.9400133 2.1411329 2.5405731 8.3610685 8.3640777
19 IRF7 11.0179771 6.4581891 8.7380831 62.4310702 271.3422039
20 ISG15 5.8849044 7.3374561 6.6111803 75.1987989 760.8912894
21 LCN2 0.0000000 18.8243390 9.4121695 18.4188103 85.0867298
22 LTF 7.0896590 6.2654140 6.6775365 3.7497576 8.5808681
23 MMP8 0.6208191 0.5750114 0.5979153 1.8750689 35.5194204
24 MX1 42.1584688 19.0040182 30.5812435 238.3119155 661.8207628
25 NFKB1 10.7158626 10.2839859 10.4999243 14.6977217 16.8861111
26 OAS2 11.6362280 4.4306470 8.0334375 54.8586099 278.4500008
27 OLFM4 1.6548218 2.7519279 2.2033748 0.7736589 2.6757977
28 PTX3 7.0078139 2.8148602 4.9113371 8.8142195 55.0447852
29 S100A11 318.5693418 521.4542757 420.0118088 861.4947376 1282.6111320
30 S100A12 20.2528393 22.5954252 21.4241322 35.1689593 184.4817557
31 SOD2 754.3956834 860.3837563 807.3897199 1084.2784120 3172.2849990
32 STAT2 67.0692967 31.5823938 49.3258453 124.0432856 197.0298805
33 TNFSF10 23.8957126 10.7456840 17.3206983 45.8979336 44.1594543
34 CD1C 28.7184764 38.7325455 33.7255109 11.5980794 4.6301144
35 CD27 50.4833614 14.1740391 32.3287002 49.4347102 11.6217238
36 CD79B 19.8054474 39.9214809 29.8634642 12.9977392 0.1055974
37 CD96 9.7728018 11.6457940 10.7092979 8.8142195 3.7450239
38 FAIM3 64.1559925 40.4671014 52.3115469 32.6850731 0.5410724
39 IL7R 166.5472310 65.3179021 115.9325666 83.0766330 52.3780669
40 SIRT1 27.3920591 22.2700232 24.8310411 13.4161022 9.3833734
41 TBX21 34.9000018 6.7482343 20.8241180 26.9616722 13.5990131
42 TGFBR1 144.5846765 115.3770316 129.9808541 111.8861236 31.8462764
X195_d6 X195_d8 X196_d0 X196_d3 X196_d6 X196_d14
1 1770.088839 900.997936 611.533092 1.745213e+03 1542.9382170 268.184209
2 120.332328 169.342450 2.214308 1.473392e+01 75.8325792 1.006293
3 316.409370 193.033585 66.148585 1.185738e+02 260.3032719 41.748385
4 254.422798 26.109481 11.398334 2.610083e+02 101.8260606 24.016255
5 159.557008 140.116920 21.310315 1.828706e+02 109.8631210 33.365024
6 196.331980 139.291412 189.994739 2.503433e+01 90.2039297 69.677671
7 334.987823 387.965174 39.047288 1.006670e+02 318.9341561 70.675577
8 368.147788 110.912831 32.366272 2.184867e+02 383.5147044 39.213588
9 160.540518 48.480214 7.284998 1.912220e+01 118.5366774 4.303871
10 514.886508 160.676312 108.754574 4.707897e+02 448.6035243 79.845019
11 38.774045 13.188306 1.203508 6.210109e+00 11.1177415 1.883886
12 416.075240 236.342651 43.580901 3.726592e+01 387.4970916 44.480880
13 479.363943 173.603534 74.941057 2.072476e+02 300.5079486 46.401970
14 2902.569797 1571.787573 402.290358 4.362891e+03 4261.8878420 354.780292
15 1551.288438 1496.836789 405.615373 1.469943e+03 1290.2761920 205.139778
16 10.608640 18.197374 4.785328 1.521799e+01 0.0000000 7.393959
17 653.459827 121.681976 6.445934 3.445200e+01 557.9263031 6.892605
18 41.179056 38.731428 12.085298 7.298761e+00 13.4567682 1.618228
19 353.822394 305.317602 54.129672 1.899954e+02 385.3499660 48.912458
20 4037.495071 733.438467 190.567800 1.168211e+03 6096.3079620 180.229116
21 884.249424 947.300923 3.523634 0.000000e+00 97.8786705 113.464711
22 20.305991 18.593146 4.391149 3.141760e+01 13.4545284 129.277537
23 142.174051 153.301312 4.897325 1.540301e+01 50.2468193 19.987517
24 1788.493935 961.903733 255.839390 4.621313e+02 1797.5184120 152.743010
25 32.059194 31.368063 23.142661 3.168688e+01 23.5642209 12.006749
26 464.918044 326.815916 74.762922 4.725247e+02 512.2009610 54.503223
27 39.354727 158.626561 0.000000 1.092100e+01 30.4650795 5.538303
28 138.452888 23.040699 7.376594 3.876906e+01 76.1276130 9.366708
29 915.879269 989.110948 731.722588 7.810043e+02 754.7875230 614.773364
30 549.098736 277.839643 2.932736 1.048967e+02 220.1251640 51.216945
31 6113.267828 4095.383462 892.579450 2.795148e+03 2765.0511240 495.547386
32 421.612292 355.768396 51.623522 2.024682e+02 307.2956973 68.731649
33 177.073027 53.355099 47.840935 8.057623e+01 333.9168552 40.354028
34 14.160640 3.615434 38.980480 2.083415e+01 0.1692049 13.650734
35 4.130501 11.612805 24.884623 5.056138e+00 0.0000000 9.246209
36 2.909372 18.193664 10.699550 3.273306e-01 19.4995205 8.693407
37 3.378296 1.911674 4.881569 0.000000e+00 3.6823030 2.760714
38 9.755564 30.913763 26.269642 5.241296e+00 13.7151766 7.785814
39 25.171147 57.849275 152.292226 4.560237e+01 41.4849572 37.432737