modified RNA-seq.R in R (69f0236f) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+7 −6

Original line number	Diff line number	Diff line
		@@ -477,9 +477,8 @@ sub_volcano_plot <- function(

		rnaseqqc <- function(
		count_file,
		sample = NA,
		name = NA,
		group = NA,
		organism = "human",
		count_type = "star",
		plot_type = "mds"
		){
		@@ -496,10 +495,12 @@ rnaseqqc <- function(
		}
		g.color <- as.character(g.color)
		}

		if(is.na(sample) \| length(sample) != length(count_file)){
		sample <- gsub("_ReadsPerGene.out.tab","",count_file)
		if(length(name) == 1){
		if(is.na(name)){
		name <- base_name(count_file,"ReadsPerGene.out.tab")
		}
		}


		if(tolower(count_type) == "star"){
		cols <- c(1, 2)
		@@ -526,7 +527,7 @@ rnaseqqc <- function(
		cpm(log = T)

		if(plot_type == "mds"){
		plotMDS(x, labels = sample,col = g.color)
		limma::plotMDS(x, labels = sample,col = g.color)
		}else if(plot_type == "glmds"){
		Glimma::glMDSPlot(x, labels = sample, launch = F,groups = group)
		print("figure saved in ./glimma-plots")