Skip to content
Snippets Groups Projects
Commit 554d4d1b authored by thierry balliau's avatar thierry balliau
Browse files

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

parents 81e2c73c 434d31af
No related branches found
No related tags found
No related merge requests found
......@@ -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))
......
......@@ -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)}
......
......@@ -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
......
......@@ -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)
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment