library(MCQR)
### Installation script for mcqr
## internal variable to modify depending on R version and current mcqr version
Rminrequirement <- "4.0.0"
packages =  c("plyr", "dplyr", "car", "cpp11", "stringr", "readODS", "VIM", "ade4", "gplots", "clValid", "agricolae", "ggplot2", "RColorBrewer", "plotly", "data.table", "nlme", "ggVennDiagram", "dataverse")
checkPackageAndInstallIt <- function(libraries, osName){
result = TRUE
installedPackages<- rownames(installed.packages())
for(mylib in libraries){
if(!(mylib %in% installedPackages)){
cat(paste0("installing ", mylib, " Package\n"))
if (osName=="windows"){
tryCatch({
install.packages(mylib, type="binary", quiet=TRUE, )
}, error = function(cond){
install.packages(mylib,  quiet=TRUE)
})
}else{
install.packages(mylib, quiet=TRUE)
}
}else{
cat(paste0(mylib, " Package is already installed, skip it\n"))
}
}
return(result)
}
install_MCQR <- function(prepare=FALSE){
# Check environnment
os <- Sys.info()
cat("Operating System\n")
cat(paste0(os['sysname'], " ", os['release'], " ", os['version'], "\n"))
cat(paste0("Machine type : ", os['machine'], "\n"))
### checking R version for listing of necessary packages
RVersion <- R.Version()
cat(paste0(RVersion$version.string, "\n"))
## specific installation depending on R version
if(as.integer(RVersion$major)<4){
stop(cat(paste0("Sorry your R version is too old for the MCQR Package, the minimum requirement is R version",Rminrequirement, "\n")))
}
## check and install needed packages
## cat("for windows install prefer binary install instead of source install\n")
test = checkPackageAndInstallIt(packages, os["sysname"])
# build_info <- rcmd("build", cmdargs = c("--as-cran", "MCQR"))
# # build_info <- unlist(strsplit(build_info$stdout, '\n'))
# print(build_info$stdout)
if(!prepare){
#Install MCQR
if("MCQR" %in% rownames(installed.packages())){
cat("MCQR was already installed. Removing it\n")
remove.packages("MCQR")
}
cat("Installing latest version of MCQR\n")
install.packages('https://forgemia.inra.fr/-/project/1534/uploads/6550076d01dab32a562598f355b17938/MCQR_1.0.2.tar.gz', repos = NULL, type = 'source')
}
}
data("iris")
force(iris)
library(ggplot2)
setwd("~/groupingprotein/test")
peptide_in_group <- read.table("peptide_list.tsv", header=T, dec=".", sep="\t", stringsAsFactors = F)
protein_mcqr <- read.table("../doc/protein_mcqr.tsv", header=T, dec=".", sep="\t", stringsAsFactors = F)
protein_mcqr <- read.table("../doc/protein_mcqr.tsv", header=T, dec=".", sep="\t", stringsAsFactors = F, quote = "'")
View(protein_mcqr)
protein_mcqr <- read.table("../doc/protein_mcqr.tsv", header=T, dec=".", sep="\t", stringsAsFactors = F, quote = "'")
specif_mcqr <- setdiff(unique(protein_mcqr$peptide), peptide_in_group$peptide_in_group)
specif_grouping <- setdiff(peptide_in_group$peptide_in_group, unique(protein_mcqr$peptide))
length(unique(peptide_in_group$peptide_in_group))
length(unique(protein_mcqr$peptide))
protein_mcqr <- read.table("protein_mcqr.tsv", header=T, dec=".", sep="\t", stringsAsFactors = F, quote = "'")
protein_mcqr <- read.table("protein_mcqr.tsv", header=T, dec=".", sep="\t", stringsAsFactors = F, quote = '"')
length(unique(protein_mcqr$peptide))
