SamToBed {esATAC} | R Documentation

## Convert SAM file to BED file

### 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

    atacSamToBed(atacProc, reportOutput = NULL, merge = c("auto", "yes", "no"),
      posOffset = +4, negOffset = -5, chrFilterList = "chrM",
      samInput = NULL, bedOutput = NULL, sortBed = TRUE, minFragLen = 0,
      maxFragLen = 100, saveExtLen = FALSE, uniqueBed = TRUE, ...)

    ## S4 method for signature 'ATACProc'
    atacSamToBed(atacProc, reportOutput = NULL,
      merge = c("auto", "yes", "no"), posOffset = +4, negOffset = -5,
      chrFilterList = "chrM", samInput = NULL, bedOutput = NULL,
      sortBed = TRUE, minFragLen = 0, maxFragLen = 100, saveExtLen = FALSE,
      uniqueBed = TRUE, ...)

    samToBed(samInput, reportOutput = NULL, merge = c("auto", "yes", "no"),
      posOffset = +4, negOffset = -5, chrFilterList = "chrM",
      bedOutput = NULL, sortBed = TRUE, minFragLen = 0, maxFragLen = 100,
      saveExtLen = FALSE, uniqueBed = TRUE, ...)

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacBowtie2Mapping` `bowtie2Mapping`
`reportOutput` | `Character` scalar report file path
`merge` | `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
`samInput` | `Character` scalar. SAM file input path.
`bedOutput` | `Character` scalar. Bed file output path.
`sortBed` | `Logical` scalar Sort bed file in the order of chromatin, start, end
`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 parameter related to input and output file path will be automatically obtained from `ATACProc-class` object(`atacProc`) or generated based on known parameters if their values are default(e.g. `NULL`). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use `samToBed` instead.

### Value

An invisible `ATACProc-class` object scalar for downstream analysis.

### Author(s)

Zheng Wei

### See Also

`atacBowtie2Mapping` `bowtie2Mapping` `atacFragLenDistr` `atacExtractCutSite` `atacPeakCalling` `atacBedUtils` `atacTSSQC` `atacBedToBigWig`

### Examples

    library(R.utils)
    library(magrittr)
    td <- tempdir()
    options(atacConf=setConfigure("tmpdir",td))

    sambzfile <- system.file(package="esATAC", "extdata", "Example.sam.bz2")
    samfile <- file.path(td,"Example.sam")
    bunzip2(sambzfile,destname=samfile,overwrite=TRUE,remove=FALSE)
    samToBed(samInput = samfile)

[Package esATAC version 1.0.23 Index]