Merge pull request #241 from MoTrPAC/develop

MotrpacBicQC 0.9.5: proteomics tmt-18 support
MoTrPAC · May 23, 2024 · e48e4cb · e48e4cb
2 parents cb17a64 + 9f1790b
commit e48e4cb
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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: 0.9.4
-Date: 2024-05-16
+Version: 0.9.5
+Date: 2024-05-22
 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 0.9.5 (2024-05-22)
+
+* Proteomics: provide QC support for TMT-18
+
 # MotrpacBicQC 0.9.4 (2024-05-16)
 
 * Enhance and improve `dl_read_gcp`: 

diff --git a/R/misc.R b/R/misc.R
@@ -343,6 +343,10 @@ filter_required_columns <- function(df,
         emeta_sample_coln <- append(emeta_sample_coln, "tmt16_channel")
         if(verbose) message("  + (+) All required columns present (tmt16 experiment)")
         df <- subset(df, select = emeta_sample_coln)
+      }else if("tmt18_channel" %in% colnames(df)){
+        emeta_sample_coln <- append(emeta_sample_coln, "tmt18_channel")
+        if(verbose) message("  + (+) All required columns present (tmt18 experiment)")
+        df <- subset(df, select = emeta_sample_coln)
       }else{
         if(verbose) message("   - (-) Expected COLUMN NAMES are missed: FAIL")
       }

diff --git a/R/proteomics_qc.R b/R/proteomics_qc.R
@@ -523,8 +523,11 @@ check_vial_metadata_proteomics <- function(df_vm,
   }else if("tmt16_channel" %in% colnames(df_vm)){
     required_columns <- c("vial_label", "tmt_plex", "tmt16_channel") 
     tmt_channel <- "tmt16_channel"
+  }else if("tmt18_channel" %in% colnames(df_vm)){
+    required_columns <- c("vial_label", "tmt_plex", "tmt18_channel") 
+    tmt_channel <- "tmt18_channel"
   }else{
-    if(verbose) message("      - (-) `tmt[11|16]_channel` column not found")
+    if(verbose) message("      - (-) `tmt[11|16|18]_channel` column not found")
     ic_vm <- 3
     return(ic_vm)
   }
@@ -542,6 +545,9 @@ check_vial_metadata_proteomics <- function(df_vm,
   }else if("tmt16_channel" %in% colnames(df_vm)){
     df_vm$vial_label <- gsub(" ", "", df_vm$vial_label)
     valid_channels <- c("126C", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N", "131C", "132N", "132C", "133N", "133C", "134N")
+  }else if("tmt18_channel" %in% colnames(df_vm)){
+    df_vm$vial_label <- gsub(" ", "", df_vm$vial_label)
+    valid_channels <- c("126C", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N", "131C", "132N", "132C", "133N", "133C", "134N")
   }
 
   ic_vm <- 0
@@ -550,7 +556,7 @@ check_vial_metadata_proteomics <- function(df_vm,
 
   for(p in plexes){
     temp_plex <- df_vm[which(df_vm$tmt_plex == p),]
-    if(all(valid_channels %in% temp_plex[[tmt_channel]])){
+    if( all(valid_channels %in% temp_plex[[tmt_channel]]) ){
       if(verbose) message("   + (+) All ", tmt_channel," channels are valid in plex ", paste(p))
     }else{
       if(tmt_channel == "tmt11_channel"){
@@ -566,15 +572,22 @@ check_vial_metadata_proteomics <- function(df_vm,
       }
     }
   }
-
-  all_samples <- df_vm$vial_label
-  all_vial_labels <- NA
-
-  if( any( grepl("Ref", df_vm$vial_label) ) ){
-    all_vial_labels <- all_samples[!grepl('^Ref', all_samples)]
-  }else{
-    if(verbose) message("      - (-) Ref channels not found in vial_metadata")
-    ic_vm <- ic_vm + 1
+
+  # Check that all plexes have one channel
+  for(p in plexes){
+    temp_plex <- df_vm[which(df_vm$tmt_plex == p),]
+    if( sum(grepl("Ref", temp_plex$vial_label)) == 1 ){
+      if(verbose) message("   + (+) Ref channel found in plex ", paste(p))
+    }else if(sum(grepl("Ref", temp_plex$vial_label)) == 0) {
+      if(verbose) message("      - (-) Ref channel missed in plex ", paste(p))
+      ic_vm <- ic_vm + 1
+    }else if(sum(grepl("Ref", temp_plex$vial_label)) > 1) {
+      if(verbose) message("      - (-) Too many reference channels in plex ", paste(p))
+      if(verbose){
+        print(temp_plex[grepl("Ref", temp_plex$vial_label), ])
+      }
+      ic_vm <- ic_vm + 1
+    }
   }
 
   if( any(duplicated(df_vm$vial_label)) ){

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="2024-05-16">
+<meta name="date" content="2024-05-22">
 <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> 2024-05-16</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-05-22</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="2024-05-16">
+<meta name="date" content="2024-05-22">
 <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> 2024-05-16</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-05-22</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="2024-05-16">
+<meta name="date" content="2024-05-22">
 <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> 2024-05-16</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-05-22</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="2024-05-16">
+<meta name="date" content="2024-05-22">
 <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> 2024-05-16</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-05-22</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: 2024-05-16T19:23Z
+last_built: 2024-05-23T04:49Z
 
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