v0.5.9: bug fixes affecting human and pass1c

MoTrPAC · Aug 11, 2021 · 11df94d · 11df94d
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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: 0.5.8
-Date: 2021-08-06
+Version: 0.5.9
+Date: 2021-08-10
 Author: MoTrPAC Bioinformatics Center
 Maintainer: David Jimenez-Morales <davidjm@stanford.edu>
 Description: R Package for the analysis of MoTrPAC datasets. 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# MotrpacBicQC 0.5.9 (2021-08-10)
+
+* Adjustments for PASS1C-06
+* Bug fixes affecting HUMAN phase processing
+
 # MotrpacBicQC 0.5.8 (2021-08-06)
 
 * New Metabolomics QC plots: number and proportion of named vs unnamed features identified

diff --git a/R/metabolomics_qc.R b/R/metabolomics_qc.R
@@ -553,6 +553,12 @@ validate_metabolomics <- function(input_results_folder,
   phase <- validate_phase(input_results_folder)
   tissue_code <- validate_tissue(input_results_folder)
   batch_folder <- validate_batch(input_results_folder)
+
+  if( !is.null(dmaqc_phase2validate) ){
+    phase2check <- dmaqc_phase2validate
+  }else{
+    phase2check <- phase
+  }
 
   # issue_count-----
   ic <- 0
@@ -574,10 +580,10 @@ validate_metabolomics <- function(input_results_folder,
 
   input_results_folder <- normalizePath(input_results_folder)
 
-  input_folder_short <- regmatches(input_results_folder, regexpr("PASS.*PROCESSED_[0-9]{8}", input_results_folder))
+  input_folder_short <- regmatches(input_results_folder, regexpr("(HUMAN|PASS).*PROCESSED_[0-9]{8}", input_results_folder))
   if(is_empty(input_folder_short)){
     if(verbose) message("\nThe PROCESSED_YYYYMMDD folder full path is not correct. Example:")
-    if(verbose) message("/full/path/to/folder/PASS1A-06/T66/RPNEG/BATCH1_20190822/PROCESSED_202003")
+    if(verbose) message("/full/path/to/folder/PASS1A-06/T66/RPNEG/BATCH1_20190822/PROCESSED_20200302")
     stop("Input folder not according to guidelines")
   }
 
@@ -760,7 +766,7 @@ validate_metabolomics <- function(input_results_folder,
 
     if(verbose) message("\n\n## QC Plots\n")
 
-    output_prefix <- paste0(cas, ".", tolower(phase), ".", tissue_code, ".",tolower(assay), ".", tolower(processfolder))
+    output_prefix <- paste0(cas, ".", tolower(phase2check), ".", tissue_code, ".",tolower(assay), ".", tolower(processfolder))
 
     if(f_rmn & f_msn ){
       r_m_n$id_type <- "named"
@@ -996,11 +1002,6 @@ validate_metabolomics <- function(input_results_folder,
   if( is.na(ic_vl) ){
     if(f_msn){
       vl_results <- m_s_n$sample_id[which(m_s_n$sample_type == "Sample")]
-      if( !is.null(dmaqc_phase2validate) ){
-        phase2check <- dmaqc_phase2validate
-      }else{
-        phase2check <- phase
-      }
       ic_vl <- check_viallabel_dmaqc(vl_submitted = vl_results,
                                      tissue_code = tissue_code,
                                      cas = cas,
@@ -1030,7 +1031,7 @@ validate_metabolomics <- function(input_results_folder,
     if(verbose) message("\nTOTAL NUMBER OF ISSUES: ", total_issues,"\n")
     if(full_report){
       reports <- data.frame(cas = cas,
-                            phase= phase,
+                            phase= phase2check,
                             tissue = tissue_code,
                             t_name = t_name,
                             assay = assay,

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="2021-08-06">
+<meta name="date" content="2021-08-11">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.9/header-attrs.js"></script><script src="other_functions_files/jquery-1.11.3/jquery.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="hasAnchor">
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-08-06</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-08-11</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="2021-08-06">
+<meta name="date" content="2021-08-11">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.9/header-attrs.js"></script><script src="qc_metabolomics_files/jquery-1.11.3/jquery.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">
@@ -191,7 +191,7 @@ <h1 class="hasAnchor">
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-08-06</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-08-11</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="2021-08-06">
+<meta name="date" content="2021-08-11">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.9/header-attrs.js"></script><script src="qc_proteomics_files/jquery-1.11.3/jquery.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">
@@ -191,7 +191,7 @@ <h1 class="hasAnchor">
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-08-06</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-08-11</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
@@ -5,5 +5,5 @@ articles:
   other_functions: other_functions.html
   qc_metabolomics: qc_metabolomics.html
   qc_proteomics: qc_proteomics.html
-last_built: 2021-08-06T23:18Z
+last_built: 2021-08-11T17:35Z
 
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_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_samples.html b/docs/reference/check_metadata_samples.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_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
diff --git a/docs/reference/check_viallabel_dmaqc.html b/docs/reference/check_viallabel_dmaqc.html
diff --git a/docs/reference/combine_metabolomics_batch.html b/docs/reference/combine_metabolomics_batch.html
diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html
diff --git a/docs/reference/get_and_validate_mdd.html b/docs/reference/get_and_validate_mdd.html
diff --git a/docs/reference/group_abbr.html b/docs/reference/group_abbr.html
diff --git a/docs/reference/group_cols.html b/docs/reference/group_cols.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/load_metabolomics_batch.html b/docs/reference/load_metabolomics_batch.html