rename gtf to c.gtf (784845ae) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+4 −4

Original line number	Diff line number	Diff line
		@@ -34,12 +34,12 @@ c.rnaseq <- function(
		x$samples$group <- group

		if(count_type %in% c("star","featurecounts")){
		gtf_info <- gtf(organism,"gene") %>%
		gtf_info <- c.gtf(organism,"gene") %>%
		as.data.table() %>%
		.[,.(gene_id,gene_name,type = gene_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		}else if(count_type == "salmon"){
		gtf_info <- gtf(organism,"transcript") %>%
		gtf_info <- c.gtf(organism,"transcript") %>%
		as.data.table() %>%
		.[,.(gene_id = transcript_id,gene_name = transcript_name,type = transcript_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		@@ -703,12 +703,12 @@ c.rnaseq_multi <- function(

		if(is.null(gtf_dt)){
		if(count_type %in% c("star","featurecounts")){
		gtf_dt <- gtf(organism,"gene") %>%
		gtf_dt <- c.gtf(organism,"gene") %>%
		as.data.table() %>%
		.[,.(gene_id,gene_name,type = gene_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		}else if(count_type == "salmon"){
		gtf_dt <- gtf(organism,"transcript") %>%
		gtf_dt <- c.gtf(organism,"transcript") %>%
		as.data.table() %>%
		.[,.(gene_id = transcript_id,gene_name = transcript_name,type = transcript_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)

+1 −1

Original line number	Diff line number	Diff line
		@@ -17,7 +17,7 @@ dtu_analysis <- function(

		if(!dir.exists(out_dir)){dir.create(out_dir)}

		tx2gene <- gtf(organism,"transcript") \|>
		tx2gene <- c.gtf(organism,"transcript") \|>
		move_columns_to_front(
		columns = c("transcript_name", "gene_name")
		)

+1 −1

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@ tx2gene <- function(organism){
		)

		if(!file.exists(tx2gene_file)){
		tx2gene <- gtf("mouse") \|>
		tx2gene <- c.gtf("mouse") \|>
		as.data.frame() \|>
		move_columns_to_front(
		columns = c("transcript_name", "gene_name")

+1 −1

Original line number	Diff line number	Diff line
		@@ -23,7 +23,7 @@ gene_density_calc <- function(
		setkey()

		gene_info_raw <- as.data.table(
		gtf(organism,"gene")
		c.gtf(organism,"gene")
		)[
		.(chr = as.character(seqnames), start, end, gene_name,strand)
		]

+3 −3

Original line number	Diff line number	Diff line
		@@ -11,7 +11,7 @@ c.anno <- function(organism,type = NA){
		}
		}

		gtf <- function(
		c.gtf <- function(
		organism,
		type = NA
		){