Merge pull request #226 from MoTrPAC/develop

MotrpacBicQC 0.9.1: add new assay `PROT_OX`
MoTrPAC · Feb 2, 2024 · 82244f3 · 82244f3
2 parents 4cd4486 + 22a8154
commit 82244f3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MotrpacBicQC
 Type: Package
 Title: QC/QA functions for the MoTrPAC community
-Version: 0.9.0
-Date: 2024-01-04
+Version: 0.9.1
+Date: 2024-02-02
 Author: MoTrPAC Bioinformatics Center
 Maintainer: David Jimenez-Morales <davidjm@stanford.edu>
 Description: R Package for the analysis of MoTrPAC datasets. 

diff --git a/NAMESPACE b/NAMESPACE
@@ -63,7 +63,6 @@ import(progress)
 import(purrr)
 import(stringr)
 import(tidyr)
-import(utils)
 import(viridis)
 importFrom(data.table,as.data.table)
 importFrom(data.table,fread)
@@ -81,3 +80,7 @@ importFrom(readr,read_lines)
 importFrom(scales,percent)
 importFrom(stats,median)
 importFrom(stats,reorder)
+importFrom(utils,URLencode)
+importFrom(utils,read.csv)
+importFrom(utils,read.delim)
+importFrom(utils,write.table)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# MotrpacBicQC 0.9.1 (2024-02-02)
+
+* New assays: `PROT_OX`
+* Fix package conflicts
+* OLINK: write release adjustments
+
 # MotrpacBicQC 0.9.0 (2024-01-04)
 
 * Add support for OLINK datasets (check `olink_qc` vignette to find out more)

diff --git a/R/misc.R b/R/misc.R
@@ -19,7 +19,7 @@
 #' @importFrom stats median reorder
 #' @import stringr
 #' @import tidyr
-#' @import utils
+#' @importFrom utils URLencode read.csv read.delim write.table
 #' @import viridis
 #____________________________________________________________________________
 

diff --git a/R/olink_qc.R b/R/olink_qc.R
@@ -1010,7 +1010,7 @@ write_olink_releases <- function(input_results_folder,
     phase_folder_release <- phase_details
   }
 
-  output_folder <- file.path(folder_root, folder_name, phase_folder_release, "prot-ol", folder_tissue, folder_assay)
+  output_folder <- file.path(folder_root, folder_name, phase_folder_release, "proteomics-targeted", folder_tissue, folder_assay)
 
   if(!dir.exists(file.path(output_folder))){
     dir.create(file.path(output_folder), recursive = TRUE)

diff --git a/R/validations.R b/R/validations.R
@@ -254,7 +254,7 @@ check_viallabel_dmaqc <- function(vl_submitted,
 validate_assay <- function(input_results_folder){
 
   assay <- stringr::str_extract(string = input_results_folder,
-                                pattern = "(?<=T\\d{2}/)(IONPNEG|RPNEG|RPPOS|HILICPOS|LRPPOS|LRPNEG|3HIB|AA|AC_DUKE|ACOA|BAIBA|CER_DUKE|CONV|KA|NUC|OA|SPHM|OXYLIPNEG|ETAMIDPOS|AC_MAYO|AMINES|CER_MAYO|TCA|IMM_CRT|IMM_GLC|IMM_INS|PROT_PH|PROT_PR|PROT_AC|PROT_UB|PROT_OL)")
+                                pattern = "(?<=T\\d{2}/)(IONPNEG|RPNEG|RPPOS|HILICPOS|LRPPOS|LRPNEG|3HIB|AA|AC_DUKE|ACOA|BAIBA|CER_DUKE|CONV|KA|NUC|OA|SPHM|OXYLIPNEG|ETAMIDPOS|AC_MAYO|AMINES|CER_MAYO|TCA|IMM_CRT|IMM_GLC|IMM_INS|PROT_PH|PROT_PR|PROT_AC|PROT_UB|PROT_OL|PROT_OX)")
   if(is.na(assay)){
     stop("ASSAY not found in the folder structure")
   }else{

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-01-04">
+<meta name="date" content="2024-02-02">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.25/header-attrs.js"></script><script src="other_functions_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="other_functions_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -123,7 +123,7 @@ <h1 class="title">MotrpacBicQC: Other Functions</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-01-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
 
 
 

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-01-04">
+<meta name="date" content="2024-02-02">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.25/header-attrs.js"></script><script src="qc_metabolomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_metabolomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -126,7 +126,7 @@ <h1 class="title">MotrpacBicQC: Metabolomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-01-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
 
 
 

diff --git a/docs/articles/qc_olink.html b/docs/articles/qc_olink.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-01-04">
+<meta name="date" content="2024-02-02">
 <title>MotrpacBicQC: OLINK QC</title>
 <script src="qc_olink_files/header-attrs-2.25/header-attrs.js"></script><script src="qc_olink_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_olink_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: OLINK QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-01-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
 
 
 

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-01-04">
+<meta name="date" content="2024-02-02">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.25/header-attrs.js"></script><script src="qc_proteomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_proteomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Proteomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-01-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
 
 
 

diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/notes_developers.html b/docs/notes_developers.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   qc_metabolomics: qc_metabolomics.html
   qc_olink: qc_olink.html
   qc_proteomics: qc_proteomics.html
-last_built: 2024-01-05T02:40Z
+last_built: 2024-02-02T17:56Z
 
diff --git a/docs/reference/assay_abbr.html b/docs/reference/assay_abbr.html
diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html
diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html
diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html
diff --git a/docs/reference/check_crossfile_olink_validation.html b/docs/reference/check_crossfile_olink_validation.html
diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html
diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html
diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html
diff --git a/docs/reference/check_metadata_phase_file.html b/docs/reference/check_metadata_phase_file.html
diff --git a/docs/reference/check_metadata_proteins.html b/docs/reference/check_metadata_proteins.html
diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html
diff --git a/docs/reference/check_metadata_samples_olink.html b/docs/reference/check_metadata_samples_olink.html
diff --git a/docs/reference/check_missing_values.html b/docs/reference/check_missing_values.html
diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html
diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html
diff --git a/docs/reference/check_results_olink.html b/docs/reference/check_results_olink.html
diff --git a/docs/reference/check_rii_proteomics.html b/docs/reference/check_rii_proteomics.html
diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html