Commit f5047d54 authored by fc-ibb105's avatar fc-ibb105
Browse files

rename base_name to c.basename

parent 0c9ad8df

R/Decay_curve.R

+1 −1
Original line number Diff line number Diff line
@@ -18,7 +18,7 @@ cvd <- function( 
						][

							,sum(counts),.(chr1,distance)

						][

							,.(sample = base_name(x[1]),chr = chr1,distance,counts = V1)

							,.(sample = c.basename(x[1]),chr = chr1,distance,counts = V1)

						]

					},

					mc.cores = length(hic_file)

R/RNA-seq.R

+1 −1
Original line number Diff line number Diff line
@@ -619,7 +619,7 @@ rnaseqqc <- function( 


	if(length(name) == 1){

		if(is.na(name)){

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

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

		}

	}

R/chaos_topdom.R

+2 −2
Original line number Diff line number Diff line
@@ -124,7 +124,7 @@ c.topdom <- function( 
				as.data.table(

					single_result[[x]]

				)[

					,sample := base_name(hic_s)

					,sample := c.basename(hic_s)

				][

					,normalization := toupper(nor_s)

				][
@@ -209,7 +209,7 @@ chaos_topdom_original <- function( 
			as.data.table(

				single_result[[x]]

			)[

				,sample := base_name(hic_file)

				,sample := c.basename(hic_file)

			][

				,normalization := toupper(normalization)

			][

R/distribution.R

+2 −2
Original line number Diff line number Diff line
@@ -34,7 +34,7 @@ distribution <- function( 
	{

		if(is.na(ref_name))

		{

			ref_name <- base_name(ref)

			ref_name <- c.basename(ref)

		}

	}
@@ -42,7 +42,7 @@ distribution <- function( 
	{

		if(is.na(align_name))

		{

			align_name <- base_name(align)

			align_name <- c.basename(align)

		}

	}

R/gtf.R

+2 −2
Original line number Diff line number Diff line
@@ -65,7 +65,7 @@ txdb <- function( 
	txdb_file <-	file.path(

						chaos_info("data_dir"),

						paste0(

							base_name(gtf_file,".gz"),

							c.basename(gtf_file,".gz"),

							".txdb"

						)

					)
@@ -76,7 +76,7 @@ txdb <- function( 
		chaos_info("data_dir") |> chaos_create_dir()

		txdb <-	gtf_file |>

				makeTxDbFromGFF(

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

					dataSource = c.basename(gtf_file,".gz"),

					organism = organism,

					metadata = c("Genome",ref),

					chrominfo = chr_size(

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