From 1fba37b23702d7b912b281b0b50358ab48f1d8eb Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 2 Feb 2024 09:36:44 -0800 Subject: [PATCH 1/4] fix package conflicts This was creating a problem when debugging on Rstudio --- NAMESPACE | 5 ++++- R/misc.R | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 153a6d58..cf3c48c6 100644 --- 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/R/misc.R b/R/misc.R index fbd00f9f..25bdef18 100644 --- 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 #____________________________________________________________________________ From f2ce6ee0b6c61601bad64eb59f8eae237b02ecbc Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 2 Feb 2024 09:37:04 -0800 Subject: [PATCH 2/4] write release olinks adjustment --- R/olink_qc.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/olink_qc.R b/R/olink_qc.R index 4b054d32..fd8da5fe 100644 --- 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) From 5d268be855277056c3b5ff1a3ee4b282791cb7d0 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 2 Feb 2024 09:45:30 -0800 Subject: [PATCH 3/4] New proteomics assay: `PROT_OX` --- R/validations.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/validations.R b/R/validations.R index 423013d2..a0524ff0 100644 --- 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{ From 22a8154962450af7d08574cb49752be27d83c299 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 2 Feb 2024 09:58:46 -0800 Subject: [PATCH 4/4] MotrpacBicQC 0.9.1: add new assay `PROT_OX` * New assays: `PROT_OX` * Fix package conflicts * OLINK: write release adjustments --- DESCRIPTION | 4 ++-- NEWS.md | 6 ++++++ docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/articles/other_functions.html | 4 ++-- docs/articles/qc_metabolomics.html | 4 ++-- docs/articles/qc_olink.html | 4 ++-- docs/articles/qc_proteomics.html | 4 ++-- docs/authors.html | 6 +++--- docs/index.html | 2 +- docs/news/index.html | 9 ++++++++- docs/notes_developers.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/assay_abbr.html | 2 +- docs/reference/assay_codes.html | 2 +- docs/reference/assay_order.html | 2 +- docs/reference/bic_animal_tissue_code.html | 2 +- docs/reference/check_crossfile_olink_validation.html | 2 +- docs/reference/check_failedsamples.html | 2 +- docs/reference/check_manifest_rawdata.html | 2 +- docs/reference/check_metadata_metabolites.html | 2 +- docs/reference/check_metadata_phase_file.html | 2 +- docs/reference/check_metadata_proteins.html | 2 +- docs/reference/check_metadata_samples.html | 2 +- docs/reference/check_metadata_samples_olink.html | 2 +- docs/reference/check_missing_values.html | 2 +- docs/reference/check_ratio_proteomics.html | 2 +- docs/reference/check_results.html | 2 +- docs/reference/check_results_olink.html | 2 +- docs/reference/check_rii_proteomics.html | 2 +- docs/reference/check_vial_metadata_proteomics.html | 2 +- docs/reference/check_viallabel_dmaqc.html | 2 +- docs/reference/combine_metabolomics_batch.html | 2 +- docs/reference/create_folder.html | 2 +- docs/reference/dl_read_gcp.html | 2 +- docs/reference/filter_required_columns.html | 2 +- docs/reference/generate_phase_details.html | 2 +- docs/reference/get_and_validate_mdd.html | 2 +- docs/reference/get_full_path2batch.html | 2 +- docs/reference/group_abbr.html | 2 +- docs/reference/group_cols.html | 2 +- docs/reference/index.html | 2 +- docs/reference/load_metabolomics_batch.html | 2 +- docs/reference/load_olink_batch.html | 2 +- docs/reference/load_proteomics.html | 2 +- docs/reference/merge_all_metabolomics.html | 2 +- docs/reference/merge_metabolomics_metadata.html | 2 +- docs/reference/merge_phenotype_metabolomics.html | 2 +- docs/reference/metabolomics_data_dictionary.html | 2 +- docs/reference/metadata_metabolites_named.html | 2 +- docs/reference/metadata_metabolites_unnamed.html | 2 +- docs/reference/metadata_sample_named.html | 2 +- docs/reference/metadata_sample_unnamed.html | 2 +- docs/reference/open_file.html | 2 +- docs/reference/phenotypes_pass1a06_short.html | 2 +- docs/reference/plot_basic_metabolomics_qc.html | 2 +- docs/reference/plot_basic_olink_qc.html | 2 +- docs/reference/proteomics_plots_rii.html | 2 +- docs/reference/remove_empty_columns.html | 2 +- docs/reference/remove_empty_rows.html | 2 +- docs/reference/results_named.html | 2 +- docs/reference/results_unnamed.html | 2 +- docs/reference/set_phase.html | 2 +- docs/reference/sex_abbr.html | 2 +- docs/reference/sex_cols.html | 2 +- docs/reference/tissue_abbr.html | 2 +- docs/reference/tissue_cols.html | 2 +- docs/reference/tissue_order.html | 2 +- docs/reference/validate_assay.html | 2 +- docs/reference/validate_batch.html | 2 +- docs/reference/validate_cas.html | 2 +- docs/reference/validate_dates_times.html | 2 +- docs/reference/validate_lc_column_id.html | 2 +- docs/reference/validate_metabolomics.html | 2 +- docs/reference/validate_na_empty.html | 2 +- docs/reference/validate_olink.html | 2 +- docs/reference/validate_phase.html | 2 +- docs/reference/validate_processFolder.html | 2 +- docs/reference/validate_proteomics.html | 2 +- docs/reference/validate_refmetname.html | 2 +- docs/reference/validate_tissue.html | 2 +- docs/reference/validate_two_phases.html | 2 +- docs/reference/validate_uniprot_ids_with_uniprot.html | 2 +- docs/reference/validate_yyyymmdd_dates.html | 2 +- docs/reference/write_metabolomics_releases.html | 2 +- docs/reference/write_olink_releases.html | 2 +- docs/reference/write_proteomics_releases.html | 2 +- 88 files changed, 107 insertions(+), 94 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index bcc123bd..405c6018 100644 --- 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 Description: R Package for the analysis of MoTrPAC datasets. diff --git a/NEWS.md b/NEWS.md index 006a7801..efb7d374 100644 --- 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/docs/404.html b/docs/404.html index 36fa00a4..415e0f95 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 960376a1..b442cdc3 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/articles/index.html b/docs/articles/index.html index e653033f..a6a47917 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html index fabfacc1..9ba58453 100644 --- a/docs/articles/other_functions.html +++ b/docs/articles/other_functions.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Other Functions @@ -123,7 +123,7 @@

MotrpacBicQC: Other Functions

-

2024-01-04

+

2024-02-02

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html index d9ab091b..029052c4 100644 --- a/docs/articles/qc_metabolomics.html +++ b/docs/articles/qc_metabolomics.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Metabolomics QC @@ -126,7 +126,7 @@

MotrpacBicQC: Metabolomics QC

-

2024-01-04

+

2024-02-02

diff --git a/docs/articles/qc_olink.html b/docs/articles/qc_olink.html index b6e49082..eb130979 100644 --- a/docs/articles/qc_olink.html +++ b/docs/articles/qc_olink.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: OLINK QC @@ -125,7 +125,7 @@

MotrpacBicQC: OLINK QC

-

2024-01-04

+

2024-02-02

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html index b60f10b6..07a77926 100644 --- a/docs/articles/qc_proteomics.html +++ b/docs/articles/qc_proteomics.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Proteomics QC @@ -125,7 +125,7 @@

MotrpacBicQC: Proteomics QC

-

2024-01-04

+

2024-02-02

diff --git a/docs/authors.html b/docs/authors.html index 9cc94bf6..894d6914 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 @@ -82,13 +82,13 @@

Citation

Center MB (2024). MotrpacBicQC: QC/QA functions for the MoTrPAC community. -R package version 0.9.0, https://github.com/MoTrPAC/MotrpacBicQC. +R package version 0.9.1, https://github.com/MoTrPAC/MotrpacBicQC. 

@Manual{,
   title = {MotrpacBicQC: QC/QA functions for the MoTrPAC community},
   author = {MoTrPAC Bioinformatics Center},
   year = {2024},
-  note = {R package version 0.9.0},
+  note = {R package version 0.9.1},
   url = {https://github.com/MoTrPAC/MotrpacBicQC},
 }
diff --git a/docs/index.html b/docs/index.html index 7dc69e85..371cb0db 100644 --- a/docs/index.html +++ b/docs/index.html @@ -41,7 +41,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/news/index.html b/docs/news/index.html index e5740a58..aac84032 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 @@ -66,6 +66,13 @@

Changelog

Source: NEWS.md +
+

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/docs/notes_developers.html b/docs/notes_developers.html index 4dea5795..a32920d9 100644 --- a/docs/notes_developers.html +++ b/docs/notes_developers.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5c7171e9..4f8161e7 100644 --- 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 index 36672dd0..74ba1eb1 100644 --- a/docs/reference/assay_abbr.html +++ b/docs/reference/assay_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html index 57ca05ce..b657261e 100644 --- a/docs/reference/assay_codes.html +++ b/docs/reference/assay_codes.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html index ae383afd..fbe10742 100644 --- a/docs/reference/assay_order.html +++ b/docs/reference/assay_order.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html index 00c64e86..252788fe 100644 --- a/docs/reference/bic_animal_tissue_code.html +++ b/docs/reference/bic_animal_tissue_code.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_crossfile_olink_validation.html b/docs/reference/check_crossfile_olink_validation.html index f356939c..4d5a69b4 100644 --- a/docs/reference/check_crossfile_olink_validation.html +++ b/docs/reference/check_crossfile_olink_validation.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html index 55810973..fa591f0e 100644 --- a/docs/reference/check_failedsamples.html +++ b/docs/reference/check_failedsamples.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html index 335e49e2..abbcada0 100644 --- a/docs/reference/check_manifest_rawdata.html +++ b/docs/reference/check_manifest_rawdata.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html index d1c9f611..3b7dbf8f 100644 --- a/docs/reference/check_metadata_metabolites.html +++ b/docs/reference/check_metadata_metabolites.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_metadata_phase_file.html b/docs/reference/check_metadata_phase_file.html index 75d293c1..15182268 100644 --- a/docs/reference/check_metadata_phase_file.html +++ b/docs/reference/check_metadata_phase_file.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_metadata_proteins.html b/docs/reference/check_metadata_proteins.html index d6a75d52..c5be8d49 100644 --- a/docs/reference/check_metadata_proteins.html +++ b/docs/reference/check_metadata_proteins.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html index f646877a..3cbc620a 100644 --- a/docs/reference/check_metadata_samples.html +++ b/docs/reference/check_metadata_samples.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_metadata_samples_olink.html b/docs/reference/check_metadata_samples_olink.html index e5c6e467..93de5fa2 100644 --- a/docs/reference/check_metadata_samples_olink.html +++ b/docs/reference/check_metadata_samples_olink.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_missing_values.html b/docs/reference/check_missing_values.html index 92ba06d4..86683837 100644 --- a/docs/reference/check_missing_values.html +++ b/docs/reference/check_missing_values.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html index 6fd9bf44..2abda10f 100644 --- a/docs/reference/check_ratio_proteomics.html +++ b/docs/reference/check_ratio_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html index a7ddb9a0..0c87adde 100644 --- a/docs/reference/check_results.html +++ b/docs/reference/check_results.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_results_olink.html b/docs/reference/check_results_olink.html index 21d0122d..e902613d 100644 --- a/docs/reference/check_results_olink.html +++ b/docs/reference/check_results_olink.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_rii_proteomics.html b/docs/reference/check_rii_proteomics.html index b766a05c..0c3ba799 100644 --- a/docs/reference/check_rii_proteomics.html +++ b/docs/reference/check_rii_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html index 4e9deab1..966ac50a 100644 --- a/docs/reference/check_vial_metadata_proteomics.html +++ b/docs/reference/check_vial_metadata_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/check_viallabel_dmaqc.html b/docs/reference/check_viallabel_dmaqc.html index b8b3ad56..fd9939f4 100644 --- a/docs/reference/check_viallabel_dmaqc.html +++ b/docs/reference/check_viallabel_dmaqc.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/combine_metabolomics_batch.html b/docs/reference/combine_metabolomics_batch.html index 95ad745e..30a6577d 100644 --- a/docs/reference/combine_metabolomics_batch.html +++ b/docs/reference/combine_metabolomics_batch.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/create_folder.html b/docs/reference/create_folder.html index dea4803b..cfedc793 100644 --- a/docs/reference/create_folder.html +++ b/docs/reference/create_folder.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/dl_read_gcp.html b/docs/reference/dl_read_gcp.html index 453a316e..d462e42b 100644 --- a/docs/reference/dl_read_gcp.html +++ b/docs/reference/dl_read_gcp.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html index c9ed720f..5c6f53ae 100644 --- a/docs/reference/filter_required_columns.html +++ b/docs/reference/filter_required_columns.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/generate_phase_details.html b/docs/reference/generate_phase_details.html index beb5d454..a7d20b89 100644 --- a/docs/reference/generate_phase_details.html +++ b/docs/reference/generate_phase_details.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/get_and_validate_mdd.html b/docs/reference/get_and_validate_mdd.html index 84d0fd19..e99d8232 100644 --- a/docs/reference/get_and_validate_mdd.html +++ b/docs/reference/get_and_validate_mdd.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/get_full_path2batch.html b/docs/reference/get_full_path2batch.html index 4056a7c7..0f69574d 100644 --- a/docs/reference/get_full_path2batch.html +++ b/docs/reference/get_full_path2batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/group_abbr.html b/docs/reference/group_abbr.html index 311e7047..f3331ee0 100644 --- a/docs/reference/group_abbr.html +++ b/docs/reference/group_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/group_cols.html b/docs/reference/group_cols.html index fd9e74f1..3069a058 100644 --- a/docs/reference/group_cols.html +++ b/docs/reference/group_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index d418a1cd..75de9407 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/load_metabolomics_batch.html b/docs/reference/load_metabolomics_batch.html index bcae599a..2e6ffe27 100644 --- a/docs/reference/load_metabolomics_batch.html +++ b/docs/reference/load_metabolomics_batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/load_olink_batch.html b/docs/reference/load_olink_batch.html index 7bbda3b1..4bd3a422 100644 --- a/docs/reference/load_olink_batch.html +++ b/docs/reference/load_olink_batch.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/load_proteomics.html b/docs/reference/load_proteomics.html index ca6d3ccf..3d2fd910 100644 --- a/docs/reference/load_proteomics.html +++ b/docs/reference/load_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/merge_all_metabolomics.html b/docs/reference/merge_all_metabolomics.html index 081db019..6ee306e8 100644 --- a/docs/reference/merge_all_metabolomics.html +++ b/docs/reference/merge_all_metabolomics.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/merge_metabolomics_metadata.html b/docs/reference/merge_metabolomics_metadata.html index 2c8a1d3c..6b2e6c99 100644 --- a/docs/reference/merge_metabolomics_metadata.html +++ b/docs/reference/merge_metabolomics_metadata.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/merge_phenotype_metabolomics.html b/docs/reference/merge_phenotype_metabolomics.html index f7c7488a..aa901bbe 100644 --- a/docs/reference/merge_phenotype_metabolomics.html +++ b/docs/reference/merge_phenotype_metabolomics.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/metabolomics_data_dictionary.html b/docs/reference/metabolomics_data_dictionary.html index 02b125f8..bf1f5069 100644 --- a/docs/reference/metabolomics_data_dictionary.html +++ b/docs/reference/metabolomics_data_dictionary.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/metadata_metabolites_named.html b/docs/reference/metadata_metabolites_named.html index f97c7cdf..f8c16abd 100644 --- a/docs/reference/metadata_metabolites_named.html +++ b/docs/reference/metadata_metabolites_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/metadata_metabolites_unnamed.html b/docs/reference/metadata_metabolites_unnamed.html index af01b8e6..3da459f2 100644 --- a/docs/reference/metadata_metabolites_unnamed.html +++ b/docs/reference/metadata_metabolites_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/metadata_sample_named.html b/docs/reference/metadata_sample_named.html index d085bead..c4b61b5a 100644 --- a/docs/reference/metadata_sample_named.html +++ b/docs/reference/metadata_sample_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/metadata_sample_unnamed.html b/docs/reference/metadata_sample_unnamed.html index e3edafff..51bb5615 100644 --- a/docs/reference/metadata_sample_unnamed.html +++ b/docs/reference/metadata_sample_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/open_file.html b/docs/reference/open_file.html index a246a18d..a72a2aa3 100644 --- a/docs/reference/open_file.html +++ b/docs/reference/open_file.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/phenotypes_pass1a06_short.html b/docs/reference/phenotypes_pass1a06_short.html index 05022c80..436273e8 100644 --- a/docs/reference/phenotypes_pass1a06_short.html +++ b/docs/reference/phenotypes_pass1a06_short.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/plot_basic_metabolomics_qc.html b/docs/reference/plot_basic_metabolomics_qc.html index 5f08f6f9..74e16e87 100644 --- a/docs/reference/plot_basic_metabolomics_qc.html +++ b/docs/reference/plot_basic_metabolomics_qc.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/plot_basic_olink_qc.html b/docs/reference/plot_basic_olink_qc.html index e1f7d09e..e773a14e 100644 --- a/docs/reference/plot_basic_olink_qc.html +++ b/docs/reference/plot_basic_olink_qc.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/proteomics_plots_rii.html b/docs/reference/proteomics_plots_rii.html index b739dfdf..d493f652 100644 --- a/docs/reference/proteomics_plots_rii.html +++ b/docs/reference/proteomics_plots_rii.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/remove_empty_columns.html b/docs/reference/remove_empty_columns.html index c68e0c4d..feddb96a 100644 --- a/docs/reference/remove_empty_columns.html +++ b/docs/reference/remove_empty_columns.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/remove_empty_rows.html b/docs/reference/remove_empty_rows.html index 80555236..663a354c 100644 --- a/docs/reference/remove_empty_rows.html +++ b/docs/reference/remove_empty_rows.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/results_named.html b/docs/reference/results_named.html index 67298af3..4207a30c 100644 --- a/docs/reference/results_named.html +++ b/docs/reference/results_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/results_unnamed.html b/docs/reference/results_unnamed.html index c0ddacd0..3c901b9e 100644 --- a/docs/reference/results_unnamed.html +++ b/docs/reference/results_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/set_phase.html b/docs/reference/set_phase.html index 853fe4d5..5ad6834e 100644 --- a/docs/reference/set_phase.html +++ b/docs/reference/set_phase.html @@ -27,7 +27,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/sex_abbr.html b/docs/reference/sex_abbr.html index 36dd5163..b6f6dfca 100644 --- a/docs/reference/sex_abbr.html +++ b/docs/reference/sex_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/sex_cols.html b/docs/reference/sex_cols.html index 2dbb9ed8..3a14764d 100644 --- a/docs/reference/sex_cols.html +++ b/docs/reference/sex_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/tissue_abbr.html b/docs/reference/tissue_abbr.html index 83bf0d6f..acaefdf6 100644 --- a/docs/reference/tissue_abbr.html +++ b/docs/reference/tissue_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/tissue_cols.html b/docs/reference/tissue_cols.html index bfa0f378..675965dd 100644 --- a/docs/reference/tissue_cols.html +++ b/docs/reference/tissue_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/tissue_order.html b/docs/reference/tissue_order.html index cbb7a658..db5d4ff4 100644 --- a/docs/reference/tissue_order.html +++ b/docs/reference/tissue_order.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_assay.html b/docs/reference/validate_assay.html index 82da824b..18361ea3 100644 --- a/docs/reference/validate_assay.html +++ b/docs/reference/validate_assay.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_batch.html b/docs/reference/validate_batch.html index f16b3020..3f0c0d16 100644 --- a/docs/reference/validate_batch.html +++ b/docs/reference/validate_batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_cas.html b/docs/reference/validate_cas.html index 06af839a..4cf4e66e 100644 --- a/docs/reference/validate_cas.html +++ b/docs/reference/validate_cas.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_dates_times.html b/docs/reference/validate_dates_times.html index 708e6ac2..9b2b91f2 100644 --- a/docs/reference/validate_dates_times.html +++ b/docs/reference/validate_dates_times.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_lc_column_id.html b/docs/reference/validate_lc_column_id.html index c7cedddc..c4ae2206 100644 --- a/docs/reference/validate_lc_column_id.html +++ b/docs/reference/validate_lc_column_id.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_metabolomics.html b/docs/reference/validate_metabolomics.html index 2260dd4a..84a7dead 100644 --- a/docs/reference/validate_metabolomics.html +++ b/docs/reference/validate_metabolomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_na_empty.html b/docs/reference/validate_na_empty.html index 35e67b85..9eba2dd7 100644 --- a/docs/reference/validate_na_empty.html +++ b/docs/reference/validate_na_empty.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_olink.html b/docs/reference/validate_olink.html index 71512272..c14c9d5f 100644 --- a/docs/reference/validate_olink.html +++ b/docs/reference/validate_olink.html @@ -20,7 +20,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_phase.html b/docs/reference/validate_phase.html index 2ae96d56..7d7c64d0 100644 --- a/docs/reference/validate_phase.html +++ b/docs/reference/validate_phase.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_processFolder.html b/docs/reference/validate_processFolder.html index 1832fed4..a7057731 100644 --- a/docs/reference/validate_processFolder.html +++ b/docs/reference/validate_processFolder.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_proteomics.html b/docs/reference/validate_proteomics.html index d0cea6fe..6566229d 100644 --- a/docs/reference/validate_proteomics.html +++ b/docs/reference/validate_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_refmetname.html b/docs/reference/validate_refmetname.html index a86ae8f1..8b6967c8 100644 --- a/docs/reference/validate_refmetname.html +++ b/docs/reference/validate_refmetname.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_tissue.html b/docs/reference/validate_tissue.html index cdc79d2f..fb6fa1f3 100644 --- a/docs/reference/validate_tissue.html +++ b/docs/reference/validate_tissue.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_two_phases.html b/docs/reference/validate_two_phases.html index ee09a7df..4aa29c90 100644 --- a/docs/reference/validate_two_phases.html +++ b/docs/reference/validate_two_phases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_uniprot_ids_with_uniprot.html b/docs/reference/validate_uniprot_ids_with_uniprot.html index 6940548e..1bef597f 100644 --- a/docs/reference/validate_uniprot_ids_with_uniprot.html +++ b/docs/reference/validate_uniprot_ids_with_uniprot.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/validate_yyyymmdd_dates.html b/docs/reference/validate_yyyymmdd_dates.html index a6b32945..e93b6e24 100644 --- a/docs/reference/validate_yyyymmdd_dates.html +++ b/docs/reference/validate_yyyymmdd_dates.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/write_metabolomics_releases.html b/docs/reference/write_metabolomics_releases.html index 838343b5..9fb28ad3 100644 --- a/docs/reference/write_metabolomics_releases.html +++ b/docs/reference/write_metabolomics_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/write_olink_releases.html b/docs/reference/write_olink_releases.html index 5f981cac..431b04bb 100644 --- a/docs/reference/write_olink_releases.html +++ b/docs/reference/write_olink_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1 diff --git a/docs/reference/write_proteomics_releases.html b/docs/reference/write_proteomics_releases.html index d24788ee..4320f824 100644 --- a/docs/reference/write_proteomics_releases.html +++ b/docs/reference/write_proteomics_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.0 + 0.9.1