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Commit 75a667e1 authored by thierry Balliau's avatar thierry Balliau
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Merge branch 'master' of forgemia.inra.fr:pappso/mcqr into master

# Conflicts:
#	MCQR/R/mcq_get.R
#	MCQR/R/priv_mcq_compute_contrasts.R
parents f0440214 26513ba7
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......@@ -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))
}
......@@ -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))
})
......
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