upgrade RNAseq and bump version to 0.3.8 (78d62aef) · Commits · Chaos / chaos.tools

DESCRIPTION

+1 −1

Original line number	Diff line number	Diff line
		Package: chaos.tools
		Type: Package
		Title: Tools for Chao
		Version: 0.3.7
		Version: 0.3.8
		Author: Chao Fang
		Maintainer: Chao Fang <FC-IBB105@outlook.com>
		Description: The package contains some useful functions that I use to analyze high-throughput sequencing data.

+54 −9

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

		c.rnaseq <- function(
		c.rnaseq.core <- function(
		dge_list = NULL,
		count_files,
		group,
		@@ -214,6 +214,51 @@ c.rnaseq <- function(
		}
		}

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

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

		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
		)
		}
		) \|>
		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,