Commit eefc0e4f authored by Chaos's avatar Chaos
Browse files

change the behavior of base_name()

parent 1f4e5301

R/RNA-seq.R

+1 −1
Original line number Diff line number Diff line
@@ -487,7 +487,7 @@ rnaseqqc <- function( 


	if(length(name) == 1){

		if(is.na(name)){

			name <- base_name(count_file,"ReadsPerGene.out.tab")

			name <- base_name(count_file,".ReadsPerGene.out.tab")

		}

	}

R/chaos_topdom.R

+2 −2
Original line number Diff line number Diff line
@@ -121,7 +121,7 @@ chaos_topdom <- function( 
				as.data.table(

					single_result[[x]]

				)[

					,sample := base_name(hic_s,"hic")

					,sample := base_name(hic_s)

				][

					,normalization := toupper(nor_s)

				][
@@ -206,7 +206,7 @@ chaos_topdom_original <- function( 
			as.data.table(

				single_result[[x]]

			)[

				,sample := base_name(hic_file,"hic")

				,sample := base_name(hic_file)

			][

				,normalization := toupper(normalization)

			][

R/gtf.R

+2 −2
Original line number Diff line number Diff line
@@ -64,7 +64,7 @@ txdb <- function( 
	txdb_file <-	file.path(

						chaos_info("data_dir"),

						paste0(

							base_name(gtf_file,"gz"),

							base_name(gtf_file,".gz"),

							".txdb"

						)

					)
@@ -75,7 +75,7 @@ txdb <- function( 
		chaos_info("data_dir") |> chaos_create_dir()

		txdb <-	gtf_file |>

				makeTxDbFromGFF(

					dataSource = base_name(gtf_file,"gz"),

					dataSource = base_name(gtf_file,".gz"),

					organism = organism,

					metadata = c("Genome",ref),

					chrominfo = chr_size(

R/str_manipulation.R

+2 −2
Original line number Diff line number Diff line
@@ -21,12 +21,12 @@ base_name <- function( 
	

			if(is.na(ext))

			{

				ext <- last_str(shortname)

				ext <- paste0(".",last_str(shortname))

			}

	

			shortname |>

			gsub(

				pattern = paste0(".",ext),

				pattern = ext,

				replacement = ""

			)

		}

R/wcpa.R

+2 −2
Original line number Diff line number Diff line
@@ -222,8 +222,8 @@ wcpa_compare_plot <- function( 
						max = 1.2,

						max_color = "#e64b35"

){

	if(is.na(control_name)){control_name <- base_name(control_hic,".hic")}

	if(is.na(observe_name)){observe_name <- base_name(observe_hic,".hic")}

	if(is.na(control_name)){control_name <- base_name(control_hic)}

	if(is.na(observe_name)){observe_name <- base_name(observe_hic)}



	control_matrix <- wcpa_matrix(

						control_hic,

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