Merge pull request #170 from MoTrPAC/develop

v0.7.6: Improve DMAQC validation
MoTrPAC · Oct 27, 2022 · e5c0e00 · e5c0e00
2 parents 8fdd162 + e0558b4
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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: 0.7.5
-Date: 2022-10-21
+Version: 0.7.6
+Date: 2022-10-27
 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 +1,7 @@
+# MotrpacBicQC 0.7.6 (2022-10-27)
+
+* Improve DMAQC validation
+
 # MotrpacBicQC 0.7.5 (2022-10-21)
 
 * Update `write_proteomics` according to latest updates on data/file structure

diff --git a/R/validations.R b/R/validations.R
@@ -263,24 +263,21 @@ check_viallabel_dmaqc <- function(vl_submitted,
       # CHECK 
       samples_missed <- setdiff(dmaqc_labels, vl_submitted)
       if( !(is.null(failed_samples) & purrr::is_empty(samples_missed)) ) {
-        if(setequal(failed_samples, samples_missed)){
+        if( all(samples_missed %in% failed_samples) ){
           if(verbose) message("  + (+) DMAQC CHECK POINT: samples sent to CAS have been processed (with known issues for some samples): OK")
           ic <- "OK"
         }else{
-          # Only if it is not empty: if it is empty means that there are extra samples in the CAS site (checked below)
-          if( !purrr::is_empty(samples_missed) ){
-            samplesmissedonly <- samples_missed[!(samples_missed %in% failed_samples)]
-            if(verbose){
-              message("   - (-) DMAQC CHECK POINT: samples not found in `metadata_results`: FAIL")
-              message("\t - ", paste(samplesmissedonly, collapse = "\n\t - "))
-            }
-            missed_out <- data.frame(vial_label = samplesmissedonly)
-            missed_out$cas <- cas
-            out_plot_large <- file.path(normalizePath(out_qc_folder), paste0(outfile_missed_viallabels,"-missed_viallabels-in-cas.txt"))
-            write.table(missed_out, out_plot_large, row.names = FALSE, sep = "\t", quote = FALSE)
-            if(verbose) message("   - ( ) File `", paste0(outfile_missed_viallabels,"-missed_viallabels-in-cas.txt"), "` available with missed vial labels")
-            ic <- "FAIL"  
+          samplesmissedonly <- samples_missed[!(samples_missed %in% failed_samples)]
+          if(verbose){
+            message("   - (-) DMAQC CHECK POINT: samples not found in `metadata_results`: FAIL")
+            message("\t - ", paste(samplesmissedonly, collapse = "\n\t - "))
           }
+          missed_out <- data.frame(vial_label = samplesmissedonly)
+          missed_out$cas <- cas
+          out_plot_large <- file.path(normalizePath(out_qc_folder), paste0(outfile_missed_viallabels,"-missed_viallabels-in-cas.txt"))
+          write.table(missed_out, out_plot_large, row.names = FALSE, sep = "\t", quote = FALSE)
+          if(verbose) message("   - ( ) File `", paste0(outfile_missed_viallabels,"-missed_viallabels-in-cas.txt"), "` available with missed vial labels")
+          ic <- "FAIL"  
         }
       }else{
         if( !purrr::is_empty(samples_missed) ){

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="2022-10-21">
+<meta name="date" content="2022-10-27">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.16/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> 2022-10-21</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-27</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="2022-10-21">
+<meta name="date" content="2022-10-27">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.16/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">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Metabolomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-21</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-27</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="2022-10-21">
+<meta name="date" content="2022-10-27">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.16/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> 2022-10-21</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-27</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: 2022-10-21T19:54Z
+last_built: 2022-10-27T18:51Z
 
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/create_folder.html b/docs/reference/create_folder.html
diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html
diff --git a/docs/reference/generate_phase_details.html b/docs/reference/generate_phase_details.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