modified RNA-seq.R in R (a109c4f3) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+4 −4

Original line number	Diff line number	Diff line
		@@ -111,8 +111,8 @@ de.dt <- function(
		)
		][
		,regulation := fcase(
		log2FC > log2(fold_change) & log10P >= hyperbola_log10P,"up",
		log2FC < -log2(fold_change) & log10P >= hyperbola_log10P,"down",
		log2FC > log2(fold_change) & log10P > hyperbola_log10P, "up",
		log2FC < -log2(fold_change) & log10P > hyperbola_log10P, "down",
		default = "not_sig"
		)
		][]
		@@ -135,11 +135,11 @@ de.gene <- function(
		.data,
		fold_change,
		p_value,
		hyperbla
		hyperbola
		)

		if(re_str %in% c("up","down","not_sig"))
		sub_dt <- dt[regulation == tolower(regulation)]
		sub_dt <- dt[regulation == tolower(re_str)]
		else if(re_str == "regulated"){
		sub_dt <- dt[regulation %in% c("up","down")]
		}else{