BamToBed: Convert bam format to bed format.

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

Convert bam format to bed format.

Description

This function is used to convert SAM file to BED file and merge interleave paired end reads, shift reads, filter reads according to chromosome, filter reads according to fragment size, sort, remove duplicates reads before generating BED file.

Usage

atacBam2Bed(
  atacProc,
  bamInput = NULL,
  bedOutput = NULL,
  reportOutput = NULL,
  bsgenome = NULL,
  mergePairIntoFrag = c("auto", "yes", "no"),
  posOffset = +4,
  negOffset = -5,
  chrFilterList = "chrM|_",
  sortBed = TRUE,
  rmMultiMap = TRUE,
  minFragLen = 0,
  maxFragLen = 2000,
  saveExtLen = FALSE,
  uniqueBed = c("auto", "yes", "no"),
  ...
)

## S4 method for signature 'ATACProc'
atacBam2Bed(
  atacProc,
  bamInput = NULL,
  bedOutput = NULL,
  reportOutput = NULL,
  bsgenome = NULL,
  mergePairIntoFrag = c("auto", "yes", "no"),
  posOffset = +4,
  negOffset = -5,
  chrFilterList = "chrM|_",
  sortBed = TRUE,
  rmMultiMap = TRUE,
  minFragLen = 0,
  maxFragLen = 2000,
  saveExtLen = FALSE,
  uniqueBed = c("auto", "yes", "no"),
  ...
)

bam2bed(
  bamInput,
  bedOutput = NULL,
  reportOutput = NULL,
  bsgenome = NULL,
  mergePairIntoFrag = c("auto", "yes", "no"),
  posOffset = +4,
  negOffset = -5,
  chrFilterList = "chrM|_",
  sortBed = TRUE,
  rmMultiMap = TRUE,
  minFragLen = 0,
  maxFragLen = 2000,
  saveExtLen = FALSE,
  uniqueBed = c("auto", "yes", "no"),
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacBamSort, atacSam2Bam.
bamInput	Character scalar. Bam file input path.
bedOutput	Character scalar. Bed file output path. If ignored, bed file will be put in the same path as the bam file.
reportOutput	Character scalar. Report file path.
bsgenome	BSgenome object. This object from bioconductor
mergePairIntoFrag	Logical scalar Merge paired end reads.
posOffset	Integer scalar The offset that positive strand reads will shift.
negOffset	Integer scalar The offset that negative strand reads will shift.
chrFilterList	Character vector The chromatin(or regex of chromatin) will be discard
sortBed	Logical scalar Sort bed file in the order of chromatin, start, end
rmMultiMap	Logical scalar. Remove multi-map reads.
minFragLen	Integer scalar The minimum fragment size will be retained.
maxFragLen	Integer scalar The maximum fragment size will be retained.
saveExtLen	Logical scaler. Save the fragment that are not in the range of minFragLen and maxFragLen
uniqueBed	Logical scalar Remove duplicates reads in bed if TRUE. default: FALSE
...	Additional arguments, currently unused.

Details

The bam file wiil be automatically obtained from object(atacProc) or input by hand. Output can be ignored.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei, Wei Zhang

See Also

atacBamSort atacSam2Bam

Examples

library(Rsamtools)
# change dataset !!
# ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
# bam2bed(bamInput = ex1_file)

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.