#' Fonction qui retire les underscore dans la colonne gene des annotation
#'
#' @param species espece consernée
#' @param collicin les gènes consernés
#' @param annotationDir la localisation des fichiers d'annotations
#'
#' @return
#' @export
amelioration.annotation <- function(species,collicin,annotationDir){
library(dplyr)
collicin <- collicin$genename
collicin <- toupper(collicin)
annotationfiles <- list.files(annotationDir,full.names = T,recursive = T)
for(i in 1:length(annotationfiles))
{
currentfile <- read.csv(annotationfiles[i])
currentfile$gene <- unlist(lapply(strsplit(currentfile$gene,split='_'),function(x) x[[1]]))
write.csv(currentfile,annotationfiles[i])
print(i)
}
####### un debut pour extraire les produits des genes et les analyser
#for (i in 1:length(collicin)) {
#product <-c()
#for (j in 1:length(annotationfiles)) {
# currentfile <- read.csv(annotationfiles[j])
#currentfile$gene <- toupper(currentfile$gene)
#currentfile <- currentfile%>%filter(gene==collicin[i])
#product <- c(product,currentfile$product)
#}
#print(i)
#write.csv(table(product),paste0("99-results/","table.",collicin[i],".csv"))
#}
}
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