downsample_ChIPpeaks: Function for downsampling peaks in ChIP-data to simulate...

In carmencita/CHIC: Quality Control Pipeline for ChIP-Seq Data

Description

Function to downsample bam files: reads ChIP and Input bam files, calles peaks and removes randomly 60percent of the reads from the peaks. Returns a downsampled ChIP dataframe.

downsample_ChIPpeaks

Usage

downsample_ChIPpeaks(
  chip.data,
  input.data,
  read_length,
  annotationID = "hg19",
  mc = 1,
  debug = FALSE
)

Arguments

chip.data	data-structure with tag information reads from bam file (see readBamFile())
input.data	data-structure with tag information reads from bam file (see readBamFile())
read_length	Integer, length of the reads
annotationID	String, indicating the genome assembly (Default="hg19")
mc	Integer, the number of CPUs for parallelization (default=1)
debug	Boolean, to enter debugging mode. Intermediate files are saved in working directory

Value

chip.dataDownSampeld, data-structure with downsampled tags

Examples

## This command is time intensive to run

## To run this example code the user MUST provide 2 bam files: one for ChIP 
## and one for the input". Here we used ChIP-seq data from ENCODE. Two 
## example files can be downloaded using the following link:
## https://www.encodeproject.org/files/ENCFF000BFX/
## https://www.encodeproject.org/files/ENCFF000BDQ/
## and save them in the working directory (here given in the temporary 
## directory "filepath"

mc=4
## Not run: 

filepath=tempdir()
setwd(filepath)

data("chipSubset", package = "ChIC.data", envir = environment())
chipBam=chipSubset
data("inputSubset", package = "ChIC.data", envir = environment())
inputBam=inputSubset
chip.dataNew=downsample_ChIPpeaks(chip.data=chipBam, 
   input.data=inputBa, read_length=read_length,
   annotationID="hg19", mc=mc, debug=FALSE)

message(" downsampling from", sum(unlist(lapply(chipBam$tags,length)))," to ",
sum(unlist(lapply(chip.dataNew$tags,length))))

## End(Not run)

carmencita/CHIC documentation built on May 2, 2021, 5:09 p.m.