modified RNA-seq.R in R (4da86505) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+9 −10

Original line number	Diff line number	Diff line
		@@ -256,22 +256,22 @@ de.gene <- function(
		hyperbola
		)

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

		lapply(
		sub_dt$commpare \|> unique(),
		sub_dt$compare \|> unique(),
		\(x){
		if(keytype == "SYMBOL"){
		if(toupper(keytype) == "SYMBOL"){
		sub_dt[compare == x,gene_name]
		}else if(keytype == "ENSEMBL"){
		}else if(toupper(keytype) == "ENSEMBL"){
		sub_dt[compare == x,gene_id]
		}else if(keytype == "short_ENSEMBL"){
		}else if(toupper(keytype) == "SHORT_ENSEMBL"){
		separate_col(
		sub_dt,
		"gene_id",
		@@ -281,10 +281,9 @@ de.gene <- function(
		remove = F
		)[compare == x,short_ENSEMBL]
		}
		} \|>
		}
		) \|>
		set_names(sub_dt$commpare \|> unique())
		)

		}

		c.volcano <- function(