change export data from mcq.get.compar to unlog value and mcq.get.dataframe

creation of rd file for mcq.write

MCQR/R/mcq_get_compar.R

@@ -102,6 +102,7 @@ na.rm="ANY", columnID="ANY"), function(object, flist, na.rm, columnID){
 ## method for cmcq.protq.xic
 setMethod("mcq.get.compar", signature(object="cmcq.protq.xic", flist="ANY",
 na.rm="ANY", columnID="ANY"), function(object, flist, na.rm, columnID){
+	object@protval$q = 10^object@protval$q
 	temp = mcq.get.compar(as(object, "cmcq.generic.protq"), flist, na.rm, columnID)
 	return(temp)
 })

MCQR/R/mcq_get_dataframe.R

@@ -51,10 +51,14 @@ setMethod("mcq.get.dataframe", signature(object="cmcq.protq.peakcounting", alpha
 
 ## method for cmcq.protq.xic
 setMethod("mcq.get.dataframe", signature(object="cmcq.protq.xic", alpha="ANY"), function(object, alpha){
-	nb_pep = unique(object@protval[, c("accession", "q")])
-	colnames(nb_pep) = c("accession", "nb.pep")
+	nb_pep = unique(object@protval[, c("accession", "msrun", "count")])
+	colnames(nb_pep) = c("accession", "msrun", "nb.pep")
+	object@protval$count <- NULL
 	temp = mcq.get.dataframe(as(object, "cmcq.generic.protq"), alpha)
-	temp = merge(temp, nb_pep, by="accession")
+	temp = merge(temp, nb_pep, by=c("accession", "msrun"))
+	temp$temp_q = 10^temp$q
+	colnames(temp)[which(colnames(temp) == "q")] <- "log(q)"
+	colnames(temp)[which(colnames(temp) == "temp_q")] <- "q"
 	return(temp)
 })
 

MCQR/man/mcq.compute.tukey.Rd

@@ -22,7 +22,7 @@
 \author{PAPPSO (pappso-projetsbioinfo@groupes.renater.fr)}
 
 
-\seealso{'mcq.plot.tukey'}
+\seealso{\code{\link{mcq.plot.tukey}}}
 
 \examples{
 	\dontrun{

MCQR/man/mcq.write.Rd

+\name{mcq.write}
+
+\alias{mcq.write}
+
+\title{Write Dataframe to file}
+
+\description{This function exports an ods or a flat file containing the data containing in a dataframe create by mcq.get.dataframe, mcq.get.metadata or mcq.get.compar.}
+
+\usage{mcq.write(object, type="flat", sep="\t", dec=".", file="export")
+}
+
+\arguments{
+	\item{object}{a dataframe object.}
+	\item{type}{type of exported file : must be 'flat' for 'tsv'or 'csv' format or 'ods' for libreoffice spreadsheet format. Default value is 'flat'.}
+	\item{sep}{must be a valid column separator between ',', ';', '\\t'. Default value is '\\t'.}
+	\item{dec}{must be a valid decimal separator between ',', '.'. Default value is '.'.}
+	\item{file}{the name of the exported file without extension. Default value is 'export'.}
+}
+
+\details{This function is designed to facilitate export of data from MCQR package. It use the 'write.table' function from 'utils' packages for flat file or 'write_ods' from 'readODS' package for libreoffice spreadsheet.\\n This function does not write row names of dataframe. }
+
+
+\author{PAPPSO (pappso-projetsbioinfo@groupes.renater.fr)}
+
+
+
+\examples{
+	\dontrun{
+		data("xic_prot_imputed")
+		## retrieve data in dataframe format
+		quantification <- mcq.get.dataframe(xic_prot_imputed)
+		## save quantification result to 'tsv' file named quantification
+		mcq.write(quantification, type="flat", dec=".", sep="\t", file="quantification")
+		## retrieve metadata information
+		metadata = mcq.get.metadata(xic_prot_imputed)
+		## write metadata in libreoffice spreadsheet
+		mcq.write(quantification, type="ods", file="metadata")
+	}
+}
+
+\seealso{\code{\link{mcq.get.dataframe}}, \code{\link{mcq.get.metadata}}, \code{\link{mcq.get.compar}}, \code{\link{write_ods}}, \code{\link{write.table}}}