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

MCQR/R/mcq_drop_uncorrelated_peptides.R

@@ -49,8 +49,7 @@ mcq.drop.uncorrelated.peptides<- function (object, flist=NULL, rCutoff = 0.5) {
 
 		tab <- merge(tab, object@proteins[,c("peptide", "protein")], "peptide")
 		tabtemp <- unique(tab[,c("protein","peptiz")])
-		count <- table(tabtemp$protein)
-		proteins <- names(count[count>9])
+		proteins <- unique(tabtemp$protein)
 		nbprot.before <- length(unique(tab$protein))
 		nb.pepz.before <- length(unique(tab$peptiz))
 		nb.pep.before <- length(unique(tab$peptide))

MCQR/man/mcq.write.Rd

@@ -4,7 +4,7 @@
 
 \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.}
+\description{This function exports an ods or a flat file with the data contained in a dataframe created by mcq.get.dataframe, mcq.get.metadata or mcq.get.compar.}
 
 \usage{mcq.write(object, type="flat", sep="\t", dec=".", file="export")
 }
@@ -17,7 +17,7 @@
 	\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. }
+\details{This function is designed to facilitate export of data from MCQR. It uses 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 dataframes. }
 
 
 \author{PAPPSO (pappso-projetsbioinfo@groupes.renater.fr)}

Tools/R/script_install.R

@@ -10,7 +10,7 @@ install_version("caTools", "1.17.1.4")
 
 
 ## install dependancies
-install.packages(pkgs=c("XML", "stringr", "readODS", "VIM", "reshape2", "ade4", "multcomp", "gplots", "clValid", "agricolae", "ggplot2", "RColorBrewer", "plotly", "plyr", "dplyr", "data.table", "nlme", "ggVennDiagram"))
+install.packages(pkgs=c("stringr", "readODS", "VIM", "reshape2", "ade4", "multcomp", "gplots", "clValid", "agricolae", "ggplot2", "RColorBrewer", "plotly", "plyr", "dplyr", "data.table", "nlme", "ggVennDiagram"))
 
 
 #Install MCQR

new_example_data/script/lanceur_shotgun_strepto.R

@@ -5,11 +5,11 @@
 
 # sur PC port
 	setwd("/home/mblein/mcqr/new_example_data/")
-	install.packages('/home/mblein/mcqr/MCQR_0.5.2.tar.gz', repos = NULL, type = 'source')
+	install.packages('/home/mblein/mcqr/MCQR_0.6.0.tar.gz', repos = NULL, type = 'source')
 	load("/home/mblein/mcqr/new_example_data/input/strepto.RData")
 #sur PC moulon
 	setwd("/home/blein/Meli/Documents/mcqr/new_example_data/")
-	install.packages('/home/blein/Meli/Documents/mcqr/MCQR_0.5.2.tar.gz', repos = NULL, type = 'source')
+	install.packages('/home/blein/Meli/Documents/mcqr/MCQR_0.6.0.tar.gz', repos = NULL, type = 'source')
 	load("/home/blein/Meli/Documents/mcqr/new_example_data/input/strepto.RData")
 
 	set.seed(30)
@@ -50,6 +50,7 @@ Number of injections : 24
 3 levels for factor "time" : 72H, 48H, 36H
 4 levels for factor "rep" : C, D, B, A
 
+	#mcq.plot.rt.alignment(directory="/home/blein/Bureau/Meli/Documents/mcqr/new_example_data/input/trace", ncol=6, nrow=4, ylim=c(-200, 200)) 	
 	mcq.plot.rt.alignment(directory="/home/mblein/mcqr/new_example_data/input/trace", ncol=6, nrow=4, ylim=c(-200, 200) , file="./output/alignment.pdf" ) 
 
 	pca_on_raw_xic = mcq.compute.pca(raw_xic)