#'Check DepOIs in the fingerprint database
#'
#'@export
.CheckGeneSymbol <- function(dep.data,filename.out){
path <- system.file("extdata/",package = "Prep4DeepDEP")
load(paste0(path,"gene_fingerprints_CGP.RData"))
colnames(dep.data)[1] <- "Gene"
if(length(intersect(dep.data$Gene, fingerprint[1,])) != length(dep.data$Gene)){
list.genes <- data.frame(Gene = dep.data[which(dep.data$Gene %in% intersect(dep.data$Gene, fingerprint[1,])),1],stringsAsFactors = FALSE)
list.gene.exclude <- dep.data[which(!dep.data$Gene %in% intersect(dep.data$Gene, fingerprint[1,])),1]
list.gene.exclude <- data.frame(GeneList = list.gene.exclude, stringsAsFactors = FALSE)
write.table(list.gene.exclude, file = paste(filename.out,"fingerprint",nrow(list.gene.exclude),"excluded_genes.txt",sep = "_"),
sep = "\t",row.names = FALSE,col.names = TRUE, quote = FALSE)
#n.list.genes.exclude <- nrow(list.gene.exclude)
#n.list.genes <- nrow(list.genes)
}else{
list.genes <- data.frame( Gene = dep.data[,1],stringsAsFactors = FALSE)
}
return(list.genes)
}
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