modified RNA-seq.R in R (82679d1e) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+56 −55

Original line number	Diff line number	Diff line
		@@ -84,7 +84,7 @@ c.rnaseq.old <- function(
		.[,TSS_end := TSS_start + 1]
		}

		c.rnaseq.core <- function(
		c.rnaseq <- function(
		dge_list = NULL,
		count_files,
		group,
		@@ -214,52 +214,53 @@ c.rnaseq.core <- function(
		}
		}

		c.rnaseq <- function(
		dge_list = NULL,
		count_files,
		group,
		compare = NULL,
		organism = "human",
		gtf_dt = NULL,
		count_type = "star",
		result = "DE",
		mode = "multi"
		){
		if(tolower(mode) %in% c("single","s")){
		group_file_dt <- data.table(count_files,group)

		mclapply(
		compare,
		\(x){
		sub_group_file_dt <- group_file_dt[group %in% unlist(strsplit(x,"-"))]

		c.rnaseq.core(
		dge_list = dge_list,
		count_files = sub_group_file_dt$count_files,
		group = sub_group_file_dt$group,
		compare = x,
		organism = organism,
		gtf_dt = gtf_dt,
		count_type = count_type,
		result = result
		)
		},
		mc.cores = length(compare)
		) \|>
		rbindlist()
		}else if(tolower(mode) %in% c("multi","m")){
		c.rnaseq.core(
		dge_list = dge_list,
		count_files = count_files,
		group = group,
		compare = compare,
		organism = organism,
		gtf_dt = gtf_dt,
		count_type = count_type,
		result = result
		)
		}
		}
		## c.rnaseq <- function(
		## dge_list = NULL,
		## count_files,
		## group,
		## compare = NULL,
		## organism = "human",
		## gtf_dt = NULL,
		## count_type = "star",
		## result = "DE",
		## mode = "multi"
		## ){
		## if(tolower(mode) %in% c("single","s")){
		## group_file_dt <- data.table(count_files,group)
		##
		## mclapply(
		## compare,
		## \(x){
		## sub_group_file_dt <- group_file_dt[group %in% unlist(strsplit(x,"-"))]
		##
		## de <- c.rnaseq.core(
		## dge_list = dge_list,
		## count_files = sub_group_file_dt$count_files,
		## group = sub_group_file_dt$group,
		## compare = x,
		## organism = organism,
		## gtf_dt = gtf_dt,
		## count_type = count_type,
		## result = result
		## )
		## de
		## },
		## mc.cores = length(compare)
		## ) \|>
		## rbindlist()
		## }else if(tolower(mode) %in% c("multi","m")){
		## c.rnaseq.core(
		## dge_list = dge_list,
		## count_files = count_files,
		## group = group,
		## compare = compare,
		## organism = organism,
		## gtf_dt = gtf_dt,
		## count_type = count_type,
		## result = result
		## )
		## }
		## }

		de.dt <- function(
		.data,

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