modified 10 files in R (68f8711d) · Commits · Chaos / chaos.tools

R/Decay_curve.R

+6 −4

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@ cvd <- function(
		chr = NA
		){
		c_count <- hic_file \|>
		lapply(
		parallel::mclapply(
		function(x){
		hic_interaction(
		hic_file = x[1],
		@@ -20,7 +20,8 @@ cvd <- function(
		][
		,.(sample = base_name(x[1]),chr = chr1,distance,counts = V1)
		]
		}
		},
		mc.cores = length(hic_file)
		) \|>
		rbindlist()

		@@ -64,7 +65,7 @@ plot_cvd <- function(
		# #the contact that longer than 100Mb is rare, and we don't really need the plot the contact longer than 10Mb

		x_breaks <- log10(min):log10(max) \|>
		lapply(
		parallel::mclapply(
		function(i)
		{
		if(i < 6)
		@@ -74,7 +75,8 @@ plot_cvd <- function(
		{
		data.table(breaks = i, labels = paste0(10^(i-6),"Mb"))
		}
		}
		},
		mc.cores = length(log10(min):log10(max))
		) \|>
		rbindlist()

+3 −2

Original line number	Diff line number	Diff line
		@@ -10,9 +10,10 @@ bin <- function(
		if(length(column) == 1)
		{
		if(is.na(column)){
		column <- lapply(
		column <- parallel::mclapply(
		colnames(.data),
		function(i){if(is.numeric(dt[[i]])){i}}
		function(i){if(is.numeric(dt[[i]])){i}},
		mc.cores = length(colnames(.data))
		) \|>
		unlist()
		}

+1 −2

+9 −6

Original line number	Diff line number	Diff line
		@@ -6,21 +6,24 @@ c.topdom <- function(
		window.size = 20,
		subsample.ratio = 1
		){
		l.hic <- length(hic_files)

		info_1 <- hic_file \|>
		lapply(
		\(x){hic_info(x)[["chr"]][,hic := x][,.(hic,chr = name,length)]}
		parallel::mclapply(
		\(x){hic_info(x)[["chr"]][,hic := x][,.(hic,chr = name,length)]},
		mc.cores = l.hic
		) \|>
		rbindlist()

		info_2 <- hic_file \|>
		lapply(
		\(x)
		{
		parallel::mclapply(
		\(x){
		data.table(
		hic = x,
		chr = chr_list(hic_file = x,chr_list = chr_list)
		)
		}
		},
		mc.cores = l.hic
		) \|>
		rbindlist() \|>
		merge(info_1)

+7 −6

Original line number	Diff line number	Diff line
		@@ -315,17 +315,17 @@ distribution2 <- function(

		if(random_times > 0)
		{
		align_random <- lapply(
		align_random <- parallel::mclapply(
		1:random_times,
		function(x)
		{
		\(x){
		shuffle(
		align_real,
		ref = genome
		)[
		,exp := paste0("random_",x)
		]
		}
		},
		mc.cores = random_times
		) %>%
		rbindlist()
		random_col <- paste0("random_",1:random_times)
		@@ -468,9 +468,10 @@ location <- function(

		if(isFALSE(single))
		{
		lapply(
		parallel::mclapply(
		0:expand,
		core_func
		core_func,
		mc.cores = length(0:expand)
		) \|>
		rbindlist()
		}else