Merge branch 'master' of forgemia.inra.fr:pappso/mcqr into master

# Conflicts:
#	MCQR/R/mcq_get.R
#	MCQR/R/priv_mcq_compute_contrasts.R

MCQR/R/mcq_get.R

@@ -127,20 +127,27 @@ setMethod("mcq.get", signature(object="cmcq.generic.pepq.labeling", alpha="ANY",
 		tab <- tab[,list(protein = paste(protein, collapse=";"), accession = paste(accession, collapse=";"), protein_description = paste(protein_description, collapse=";")), by=c("peptide","fraction", "ProForma")]
 		#tab <- ddply(tab, .(peptide), summarize,  protein=paste(protein, collapse=";"), accession=paste(accession, collapse=";"), protein_description=paste(protein_description, collapse=";"))
 		tab <- rbind.data.frame(tab, object@proteins[!object@proteins$peptide %in% shared.pep,])
-		indice <- match(object@peptides$peptide, tab$peptide)
+		tab$key_get <- paste(tab$peptide, tab$fraction, sep="_")
+		temp_msrun_fraction <- object@metadata@metadata
+		temp_msrun_fraction$msrun_label <- rownames(temp_msrun_fraction)
+		temp_msrun_fraction <- temp_msrun_fraction[,c("msrun_label", "fraction")]
+		object@peptides <- merge(object@peptides, temp_msrun_fraction, by="msrun_label")
+		object@peptides$key_get <- paste(object@peptides$peptide, object@peptides$fraction, sep="_")
+		object@peptides$fraction <- NULL
+		indice <- match(object@peptides$key_get, tab$key_get)
 		object@peptides$protein <- tab$protein[indice]
 		object@peptides$accession <- tab$accession[indice]
 		object@peptides$protein_description <- tab$protein_description[indice]
 		object@peptides$fraction <- tab$fraction[indice]
 		tpep <- as.data.table(priv.mcq.get.data.with.metadata(object, meta= "both"))
-		tpep <- tpep[order(tpep$msrun,tpep$peptide),]
+		tpep <- tpep[order(tpep$msrun_label,tpep$peptide),]
 		colnames(tpep)[which(colnames(tpep)=="logarea")] <- "log10area"
 		colnames(tpep)[which(colnames(tpep)=="logratio")] <- "log10ratio"
 		colnames(tpep)[which(colnames(tpep)=="logratio.norm")] <- "log10ratio.norm"
 		## internal controle to check if no discordance in fraction are detected
 		tpep$test = tpep$fraction.x == tpep$fraction.y
 		if(FALSE %in% tpep$test){
-			stop(cat("problem of discordance between fraction in peptide data and metadata. Please contact developpers"))
+			stop("problem of discordance between fraction in peptide data and metadata. Please contact developpers")
 		}else{
 			colnames(tpep)[which(colnames(tpep)=="fraction.x")] <- "fraction"
 			tpep$fraction.y = NULL
@@ -177,17 +184,17 @@ setMethod("mcq.get", signature(object="cmcq.generic.pepq.labeling", alpha="ANY",
 })
 
 ## method for cmcq.pepq.masschroq.labeling
-setMethod("mcq.get", signature(object="cmcq.pepq.masschroq.labeling", alpha="ANY", format ="ANY", na.rm="ANY", columnID="ANY"), function(object, alpha,  format, na.rm, columnID){
-	test_argument <- .checkmcqgetArgument(object, alpha, format, na.rm, columnID)
-	if(length(test_argument$error != 0)){
-		stop(paste(test_argument$error, collapse="\n"))
-	}
-	if(length(test_argument$warning != 0)){
-		warnings(paste(test_argument$warning, collapse="\n"))
-	}
-	temp = mcq.get(as(object, "cmcq.generic.pepq.labeling"), alpha,  format, na.rm, columnID)
-	return(temp)
-})
+# setMethod("mcq.get", signature(object="cmcq.pepq.masschroq.labeling", alpha="ANY", format ="ANY", na.rm="ANY", columnID="ANY"), function(object, alpha,  format, na.rm, columnID){
+# 	test_argument <- .checkmcqgetArgument(object, alpha, format, na.rm, columnID)
+# 	if(length(test_argument$error != 0)){
+# 		stop(paste(test_argument$error, collapse="\n"))
+# 	}
+# 	if(length(test_argument$warning != 0)){
+# 		warnings(paste(test_argument$warning, collapse="\n"))
+# 	}
+# 	temp = mcq.get(as(object, "cmcq.generic.pepq.labeling"), alpha,  format, na.rm, columnID)
+# 	return(temp)
+# })
 
 ## method for cmcq.pepq.ratio.with.ref
 setMethod("mcq.get", signature(object="cmcq.pepq.ratio.with.ref", alpha="ANY", format ="ANY", na.rm="ANY", columnID="ANY"), function(object, alpha,  format, na.rm, columnID){
@@ -580,3 +587,4 @@ setMethod("mcq.get", signature(object="cmcq.cluster", alpha="ANY", format ="ANY"
 	}
 	return(list("error"=error_message, "warning"=warning_message))	
 }
+

MCQR/R/priv_mcq_get_data_with_metadata.R

@@ -162,6 +162,8 @@ setMethod("priv.mcq.get.data.with.metadata", signature(obj = "cmcq.generic.pepq.
   }else{
     result <- merge(peptides, metadata, by.x="msrun_label", by.y="Row.names")
   }
+  result$msrun <- result$msrun.x
+  result$msrun.x <- result$msrun.y <- NULL
   return(as.data.frame(result))
 })