Runnable example to the new artms_mergeEvidenceAndKeys

#37 #2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: artMS
 Type: Package
 Title: Analytical R tools for Mass Spectrometry
-Version: 0.99.12
+Version: 0.99.13
 Date: 2018-09-13
 Author: David Jimenez-Morales, John Von Dollen, Alexandre Rosa Campos
 Maintainer: David Jimenez-Morales <biodavidjm@gmail.com>

NAMESPACE

@@ -17,8 +17,7 @@ export(artms_filterEvidenceContaminants)
 export(artms_generatePhSiteExtended)
 export(artms_isEvidenceNewVersion)
 export(artms_mapUniprot2entrezGeneName)
-export(artms_mergeEvidenceKeysByFiles)
-export(artms_mergeMaxQDataWithKeys)
+export(artms_mergeEvidenceAndKeys)
 export(artms_msstats_summary)
 export(artms_plotCorumEnrichment)
 export(artms_plotHeatmapQuant)

R/MSstats_functions.R

@@ -144,25 +144,33 @@ artms_filterEvidenceContaminants <- function(data){
 # ------------------------------------------------------------------------------
 #' @title Merge evidence and keys files
 #' @description Merge the evidence and keys files on the given columns
-#' @param data The evidence in data.frame
-#' @param keys The keys in data.frame
+#' @param data (data.frame or char) The evidence data, either as adata.frame or
+#' the file name (and path)
+#' @param keys The keys data, either as a data.frame or file name (and path)
 #' @param by (vector) specifying the columns use to merge the evidence and keys.
-#' Obviously, both data.frames must have this column name.
+#' Default: `by=c('RawFile')`
 #' @return (data.frame) with the evidence and keys merged
-#' Default column to merge: `RawFile`
 #' @keywords merge, evidence, keys
-#' @examples \donttest{
-#' evidence <- read.delim("FLU-THP1-H1N1-AB-evidence.txt", stringsAsFactors = F)
-#' keys <- read.delim("FLU-THP1-H1N1-AB-keys.txt", stringsAsFactors = F)
-#' evidenceKeys <- artms_mergeMaxQDataWithKeys(data = evidence, keys = keys)
+#' @examples{
+#' evidenceKeys <- artms_mergeEvidenceAndKeys(data = artms_data_ph_evidence, 
+#'                                            keys = artms_data_ph_keys)
 #' }
 #' @export
-artms_mergeMaxQDataWithKeys <- function(data, keys, by=c('RawFile')){
+artms_mergeEvidenceAndKeys <- function(data, keys, by=c('RawFile')){
   cat(">> MERGING evidence AND keys FILES\n")
 
+  data <- .artms_checkIfFile(data)
+  keys <- .artms_checkIfFile(keys)
+
   data <- .artms_checkRawFileColumnName(data)
   keys <- .artms_checkRawFileColumnName(keys)
 
+  # Check that the keys file is correct
+  if(any(!c('RawFile','IsotopeLabelType','Condition','BioReplicate','Run') %in% colnames(keys))){ #,'SAINT','BioReplicaSaint'
+    cat('\nERROR!!! COLUMN NAMES IN keys NOT CONFORM TO SCHEMA. One of these columns is lost:\n\tRawFile\n\tIsotopeLabelType\n\tCondition\n\tBioReplicate\n\tRun\n') # \tSAINT\n\tBioReplicaSaint\n\n
+    stop('PLEASE, REVISE THE KEYS FILE AND TRY AGAIN')
+  }
+
   # Check if the number of RawFiles is the same.
   unique_data <- unique(data$RawFile)
   unique_keys <- unique(keys$RawFile)
@@ -182,59 +190,6 @@ artms_mergeMaxQDataWithKeys <- function(data, keys, by=c('RawFile')){
 }
 
 
-# ------------------------------------------------------------------------------
-#' @title Merge evidence and keys by file name
-#' 
-#' @description Merge evidence and keys by file name
-#' @param evidence_file (char) The Evidence file name
-#' @param keys_file (char) The keys file name
-#' @return (data.frame) with both evidence and keys files merged by raw.files
-#' @keywords internal, merge, evidence, keys
-#' @examples \donttest{
-#'   evidenceKeys <- artms_mergeEvidenceKeysByFiles(
-#'                   evidence_file = "FLU-THP1-H1N1-AB-evidence.txt", 
-#'                   keys_file = "FLU-THP1-H1N1-AB-keys.txt")
-#' }
-#' @export
-artms_mergeEvidenceKeysByFiles <- function(evidence_file, keys_file) {
-
-  cat(">> MERGING evidence_file AND keys_file (it might take some time)\n")
-  data <- read.delim(evidence_file, sep='\t', quote = "", header = T, stringsAsFactors = F)
-  keys <- read.delim(keys_file, sep='\t', quote = "", header = T, stringsAsFactors = F)
-
-  data <- .artms_checkRawFileColumnName(data)
-  keys <- .artms_checkRawFileColumnName(keys)
-
-  # Check that the keys file is correct
-  if(any(!c('RawFile','IsotopeLabelType','Condition','BioReplicate','Run') %in% colnames(keys))){ #,'SAINT','BioReplicaSaint'
-    cat('\nERROR!!! COLUMN NAMES IN keys NOT CONFORM TO SCHEMA. One of these columns is lost:\n\tRawFile\n\tIsotopeLabelType\n\tCondition\n\tBioReplicate\n\tRun\n') # \tSAINT\n\tBioReplicaSaint\n\n
-    cat('Please, try again once revised\n\n')
-    stop()
-  }
-
-  # MERGING THE DATA
-  # Checking that the keys make sense
-  unique_data <- unique(data$RawFile)
-  unique_keys <- unique(keys$RawFile)
-
-  # Rawfiles on Keys not found on the data
-  keys_not_found <- setdiff(unique_keys, unique_data)
-  # Rawfiles on Data not found on the keys
-  data_not_found <- setdiff(unique_data, unique_keys)
-
-  if ( (length(keys_not_found) != 0) & ( length(data_not_found) != 0) ) {
-    cat(sprintf("keys found: %s \t keys not in data file:\n%s\n", length(unique_keys)-length(keys_not_found), paste(keys_not_found,collapse='\t')))
-    cat(sprintf("data found: %s \t data not in keys file:\n%s\n", length(unique_data)-length(data_not_found), paste(data_not_found, collapse='\t')))
-    stop('\nThis script is sorry, but it needs to stop this because something is going on between your keys and evidence files so you better check\n')
-  }
-
-  ## select only required attributes from MQ format
-  datamerged <- merge(data, keys, by='RawFile')
-
-  return(datamerged)
-}
-
-
 # ------------------------------------------------------------------------------
 #' @title Convert the SILAC evidence file to MSstats format
 #' 
@@ -304,21 +259,21 @@ artms_SILACtoLong <- function(evidence_file, output){
 #' where each row represents a unique protein's results, and each column
 #' represents the comparison made by MSStats. The fold change and p-value 
 #' of each comparison will be its own column.
-#' @param evidence_file (char) Input file name and location 
+#' @param results_msstats (char) Input file name and location 
 #' (MSstats `results.txt` file)
 #' @param output_file (char) Output file name and location 
 #' (e.g. `results-wide.txt`)
 #' @return (output file tab delimited) reshaped file with unique protein ids 
 #' and as many columns log2fc and adj.pvalues as comparisons available
 #' @keywords msstats, results, wide, reshape
 #' @examples \donttest{
-#' artms_resultsWide(evidence_file = "ab-results.txt", 
+#' artms_resultsWide(results_msstats = "ab-results.txt", 
 #'                   output_file = "ab-results-wide.txt")
 #' }
 #' @export
-artms_resultsWide <- function(evidence_file, output_file){
+artms_resultsWide <- function(results_msstats, output_file){
   cat(">> PRINTING OUT MSSTATS RESULTS IN wide FORMAT\n")
-  input = fread(evidence_file, integer64 = 'double')
+  input = fread(results_msstats, integer64 = 'double')
   input_l = melt(data = input[,c('Protein', 'Label','log2FC','adj.pvalue'), with=F], id.vars = c('Protein', 'Label'))
 
   ## then cast to get combinations of LFCV/PVAl and Label as columns
@@ -432,7 +387,7 @@ artms_spectralCounts <- function(evidence_file, keys_file, output_file){
 
   if(!'IsotopeLabelType' %in% colnames(data)) data[,IsotopeLabelType:='L']
 
-  data <- artms_mergeMaxQDataWithKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
+  data <- artms_mergeEvidenceAndKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
   data_sel <- data[,c('Proteins', 'Condition', 'BioReplicate', 'Run', 'MS/MS Count'), with=F]
   setnames(data_sel, 'MS/MS Count', 'spectral_counts')
   data_sel = aggregate( spectral_counts ~ Proteins+Condition+BioReplicate+Run, data=data_sel, FUN = sum)

R/evidenceQC.R

@@ -61,7 +61,7 @@ artms_evidenceQC <- function(evidence_file,
   keys <- .artms_checkRawFileColumnName(keys)
 
   # EVIDENCE:
-  evidencekeys <- artms_mergeMaxQDataWithKeys(evidence, keys)
+  evidencekeys <- artms_mergeEvidenceAndKeys(evidence, keys)
 
   ekselecta <- aggregate(Intensity~Proteins+Condition+BioReplicate+Run, data=evidencekeys, FUN = sum)
   ekselectaBioreplica <- aggregate(Intensity~Proteins+Condition+BioReplicate, data=ekselecta, FUN = sum) 

R/evidenceToMISTformat.R

@@ -70,7 +70,7 @@ artms_evidenceToMISTformat <- function(input_file, quant_variable, keys_file, ou
 
   cat('\n\tVERIFYING DATA AND KEYS\n')
   if(!'IsotopeLabelType' %in% colnames(data)) data[,IsotopeLabelType:='L']
-  data <- artms_mergeMaxQDataWithKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
+  data <- artms_mergeEvidenceAndKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
 
   if(quant_variable == "msspc"){
     data_sel <- data[,c('Proteins','Condition','BioReplicate','Run','RawFile','ms_spectral_counts'),with=F]

R/evidenceToSaintExpressFormat.R

@@ -50,7 +50,7 @@ artms_evidenceToSaintExpressFormat <- function(input_file,
     stop('COLNAMES IN KEYS NOT CONFORM TO SCHEMA\n\tRawFile\tIsotopeLabelType\tCondition\tBioReplicate\tRun\tSAINT\n')
   } 
   if(!'IsotopeLabelType' %in% colnames(data)) data[,IsotopeLabelType:='L']
-  data <- artms_mergeMaxQDataWithKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
+  data <- artms_mergeEvidenceAndKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
   data_f <- artms_filterEvidenceContaminants(data)
   data_f <- .artms_removeMaxQProteinGroups(data_f) ## do we want this or not?
 

R/main.R

@@ -151,12 +151,12 @@ artms_quantification <- function(yaml_config_file){
         keys$Run = paste(keys$IsotopeLabelType,keys$Run , sep='')
         data$IsotopeLabelType = 'L'
         keys$IsotopeLabelType = 'L'
-        data <- artms_mergeMaxQDataWithKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
+        data <- artms_mergeEvidenceAndKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
       }else{
-        data <- artms_mergeMaxQDataWithKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
+        data <- artms_mergeEvidenceAndKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
       }
     }else{
-      data <- artms_mergeMaxQDataWithKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
+      data <- artms_mergeEvidenceAndKeys(data, keys, by = c('RawFile','IsotopeLabelType'))
     }
 
     ## fix for weird converted values from fread