Loading DESCRIPTION +1 −1 Original line number Diff line number Diff line Package: chaos.test Type: Package Title: What the Package Does (Title Case) Version: 0.3.3 Version: 0.3.4 Author: Who wrote it Maintainer: The package maintainer <yourself@somewhere.net> Description: More about what it does (maybe more than one line) Loading R/Decay_curve.R +2 −8 Original line number Diff line number Diff line Loading @@ -4,11 +4,8 @@ cvd <- function( norm = "KR", chr = NA ){ BPPARAM <- hic_file |> length() |> MulticoreParam() bpstart(BPPARAM) c_count <- hic_file |> bplapply( lapply( function(x){ hic_interaction( hic_file = x[1], Loading @@ -23,13 +20,10 @@ cvd <- function( ][ ,.(sample = base_name(x[1]),chr = chr1,distance,counts = V1) ] }, BPPARAM = BPPARAM } ) |> rbindlist() bpstop(BPPARAM) s_count <- c_count[ ,sum(counts), .(sample,distance) Loading R/bin.R +2 −8 Original line number Diff line number Diff line Loading @@ -10,17 +10,11 @@ bin <- function( if(length(column) == 1) { if(is.na(column)){ BPPARAM <- colnames(.data) |> length() |> MulticoreParam() bpstart(BPPARAM) column <- bplapply( column <- lapply( colnames(.data), function(i){if(is.numeric(dt[[i]])){i}}, BPPARAM = BPPARAM function(i){if(is.numeric(dt[[i]])){i}} ) |> unlist() bpstop(BPPARAM) } } Loading R/chr_size.R +5 −8 Original line number Diff line number Diff line Loading @@ -29,21 +29,18 @@ chr_size <- function( extra = FALSE, online = FALSE ){ chaos.tools_data_dir <- "~/.config/chaos.tools" if(!dir.exists(chaos.tools_data_dir)) { dir.create(chaos.tools_data_dir) } "data_dir" |> chaos_info() |> chaos_create_dir() local_genome_file <- system.file( "extdata", "common.genome.info.txt", package = "chaos.tools" package = chaos_info("name") ) downloaded_genome_file <- file.path( chaos.tools_data_dir, chao_data_dir, "downloaded.genome.info.txt" ) Loading R/distribution.R +2 −7 Original line number Diff line number Diff line Loading @@ -315,10 +315,7 @@ distribution2 <- function( if(random_times > 0) { BPPARAM <- 1:random_times |> MulticoreParam() bpstart(BPPARAM) align_random <- bplapply( align_random <- lapply( 1:random_times, function(x) { Loading @@ -328,11 +325,9 @@ distribution2 <- function( )[ ,exp := paste0("random_",x) ] }, BPPARAM = BPPARAM } ) %>% rbindlist() bpstop(BPPARAM) random_col <- paste0("random_",1:random_times) }else { Loading Loading
DESCRIPTION +1 −1 Original line number Diff line number Diff line Package: chaos.test Type: Package Title: What the Package Does (Title Case) Version: 0.3.3 Version: 0.3.4 Author: Who wrote it Maintainer: The package maintainer <yourself@somewhere.net> Description: More about what it does (maybe more than one line) Loading
R/Decay_curve.R +2 −8 Original line number Diff line number Diff line Loading @@ -4,11 +4,8 @@ cvd <- function( norm = "KR", chr = NA ){ BPPARAM <- hic_file |> length() |> MulticoreParam() bpstart(BPPARAM) c_count <- hic_file |> bplapply( lapply( function(x){ hic_interaction( hic_file = x[1], Loading @@ -23,13 +20,10 @@ cvd <- function( ][ ,.(sample = base_name(x[1]),chr = chr1,distance,counts = V1) ] }, BPPARAM = BPPARAM } ) |> rbindlist() bpstop(BPPARAM) s_count <- c_count[ ,sum(counts), .(sample,distance) Loading
R/bin.R +2 −8 Original line number Diff line number Diff line Loading @@ -10,17 +10,11 @@ bin <- function( if(length(column) == 1) { if(is.na(column)){ BPPARAM <- colnames(.data) |> length() |> MulticoreParam() bpstart(BPPARAM) column <- bplapply( column <- lapply( colnames(.data), function(i){if(is.numeric(dt[[i]])){i}}, BPPARAM = BPPARAM function(i){if(is.numeric(dt[[i]])){i}} ) |> unlist() bpstop(BPPARAM) } } Loading
R/chr_size.R +5 −8 Original line number Diff line number Diff line Loading @@ -29,21 +29,18 @@ chr_size <- function( extra = FALSE, online = FALSE ){ chaos.tools_data_dir <- "~/.config/chaos.tools" if(!dir.exists(chaos.tools_data_dir)) { dir.create(chaos.tools_data_dir) } "data_dir" |> chaos_info() |> chaos_create_dir() local_genome_file <- system.file( "extdata", "common.genome.info.txt", package = "chaos.tools" package = chaos_info("name") ) downloaded_genome_file <- file.path( chaos.tools_data_dir, chao_data_dir, "downloaded.genome.info.txt" ) Loading
R/distribution.R +2 −7 Original line number Diff line number Diff line Loading @@ -315,10 +315,7 @@ distribution2 <- function( if(random_times > 0) { BPPARAM <- 1:random_times |> MulticoreParam() bpstart(BPPARAM) align_random <- bplapply( align_random <- lapply( 1:random_times, function(x) { Loading @@ -328,11 +325,9 @@ distribution2 <- function( )[ ,exp := paste0("random_",x) ] }, BPPARAM = BPPARAM } ) %>% rbindlist() bpstop(BPPARAM) random_col <- paste0("random_",1:random_times) }else { Loading
