In manschmi/RMetaTools: Tools For Metagene Analysis

r format(Sys.time(), "%d %B, %Y; %R")

Setup

knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE, 
                      error=TRUE)

suppressWarnings(library('tidyverse'))
suppressWarnings(library('magrittr'))
suppressWarnings(library('knitr'))

suppressWarnings(library('rtracklayer'))
suppressWarnings(library('microbenchmark'))

deeptools matrix creation time

```{bash, eval=FALSE} conda activate deeptools3 bedfile="inst/extdata/Chen_PROMPT_TSSs_liftedTohg38.bed" plus_bw="inst/extdata/GSM1573841_mNET_8WG16_siLuc_plus_hg38.bw" minus_bw="inst/extdata/GSM1573841_mNET_8WG16_siLuc_plus_hg38.bw"

awk '$6=="+"' $bedfile > ${bedfile/.bed/_plus.bed} awk '$6=="-"' $bedfile > ${bedfile/.bed/_minus.bed}

time python ~/ms_tools/MS_Metagene_Tools/computeMatrixStranded.py reference-point -Sp $plus_bw -Sm $minus_bw -Rp ${bedfile/.bed/_plus.bed} -Rm ${bedfile/.bed/_plus.bed} -b 1000 -a 1000 --binSize=50 -o test_deeptools_mat.gz --quiet

real 0m3.875s

user 0m3.648s

sys 0m0.216s

real 0m3.892s

user 0m3.663s

sys 0m0.214s

#### select regions and a bigwig file
```r
bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")
regions <- rtracklayer::import(bedfile)

bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")

anchor = 'TSS'
upstream = 1000
downstream = 1000
window_size = 50

bw_plus <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_plus_hg38.bw", package = "RMetaTools")
bw_minus <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_minus_hg38.bw", package = "RMetaTools")

meta_tbl <- RMetaTools::metagene_matrix(bw_plus, bw_minus, bedfile, anchor, upstream, downstream, window_size)

metageneInR_fun <- function(){
  meta_tbl <- RMetaTools::metagene_matrix(bw_plus, bw_minus, bedfile, anchor, upstream, downstream, window_size)
}

benchmark import function for the 3 return types

microbenchmark(metageneInR_fun(), times = 10)

--> appears to take much less time, less than 1s !?

(meta_tbl <- RMetaTools::metagene_matrix(bw_plus, bw_minus, bedfile, anchor, upstream, downstream, window_size))

metageneInR_fun2 <- function(){
  m <- metagene_rel_anchor(bw_plus, bw_minus, bedfile, anchor, upstream, downstream, window_size)
}

microbenchmark(metageneInR_fun2(), times = 10)

sessionInfo()

manschmi/RMetaTools documentation built on Dec. 14, 2021, 4:33 a.m.