Loading NAMESPACE +1 −0 Original line number Diff line number Diff line Loading @@ -24,3 +24,4 @@ import(ggpubr) import(GenomicFeatures) import(AnnotationDbi) import(ggVennDiagram) import(parallel) R/RNA-seq.R +19 −2 Original line number Diff line number Diff line rnaseq123 <- function( c.rnaseq <- function( ctl_count_file, obs_count_file, organism = "human", Loading Loading @@ -663,7 +663,7 @@ rnaseqqc <- function( } } rnaseq123_multi <- function( c.rnaseq_multi <- function( dge_list = NULL, count_files, group, Loading Loading @@ -863,3 +863,20 @@ venn_cluster <- function( by = "gene_name" ) } c.subDE <- function( .data, compare, breaf = TRUE ){ if(isTRUE(breaf)){ common_cols <-c("gene_id","gene_name","type","adj.P.Val") }else{ common_cols <- c("gene_id","gene_name","type","chr","start","end","strand","AveExpr","F","P.Value","adj.P.Val","log10P") } final_col <- c(common_cols,compare) .data[,..final_col] |> setnames(compare,"log2FC") } No newline at end of file Loading
NAMESPACE +1 −0 Original line number Diff line number Diff line Loading @@ -24,3 +24,4 @@ import(ggpubr) import(GenomicFeatures) import(AnnotationDbi) import(ggVennDiagram) import(parallel)
R/RNA-seq.R +19 −2 Original line number Diff line number Diff line rnaseq123 <- function( c.rnaseq <- function( ctl_count_file, obs_count_file, organism = "human", Loading Loading @@ -663,7 +663,7 @@ rnaseqqc <- function( } } rnaseq123_multi <- function( c.rnaseq_multi <- function( dge_list = NULL, count_files, group, Loading Loading @@ -863,3 +863,20 @@ venn_cluster <- function( by = "gene_name" ) } c.subDE <- function( .data, compare, breaf = TRUE ){ if(isTRUE(breaf)){ common_cols <-c("gene_id","gene_name","type","adj.P.Val") }else{ common_cols <- c("gene_id","gene_name","type","chr","start","end","strand","AveExpr","F","P.Value","adj.P.Val","log10P") } final_col <- c(common_cols,compare) .data[,..final_col] |> setnames(compare,"log2FC") } No newline at end of file
