RSNPs {esATAC} | R Documentation

## Find whether snps are in the given regions.

### Description

Find snps(user providing) in given regions. This function do not consider strand.

### Usage

    atacSNPAnno(
      atacProc,
      snp.info = NULL,
      region.info = NULL,
      annoOutput = NULL,
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacSNPAnno(
      atacProc,
      snp.info = NULL,
      region.info = NULL,
      annoOutput = NULL,
      ...
    )

    snpanno(snp.info = NULL, region.info = NULL, annoOutput = NULL, ...)

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacPeakCalling` `atacMotifScan`. If from `atacPeakCalling`, the output file would contain the snps in given region. If from `atacMotifScan`, the output file would contain file path to the output of every motif.
`snp.info` | `Character` scalar. Input snp info path. There are two type of input files(you can specify by parameter withend). 1.The first 2 column must be chr, position. e.g. chr13 39776775 rs7993214. Other columns could be other information about snps. 2.The first 3 column must be chr, start, end. e.g. chr13 39776775 39776775 rs7993214. Other columns could be other information about snps. When genome is hg19, using human disease as default.
`region.info` | `Character` scalar. Input region info path. The first 3 column must be chr, position, end. The standard BED format is recommended.
`annoOutput` | `Character` scalar. Output path.
`...` | withend Your snp data has only one position column or 2.

### Value

An invisible `ATACProc-class` object scalar.

### Author(s)

Wei Zhang

### See Also

`atacPeakCalling` `atacMotifScan`

### Examples

    library(R.utils)
    p1bz <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC")
    peak1_path <- as.vector(bunzip2(filename = p1bz,
    destname = file.path(getwd(), "Example_peak1.bed"),
    ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
    snps <- system.file("extdata", "snp_info", package="esATAC")
    #snpanno(snp.info = snps, region.info = peak1_path)

[Package esATAC version 1.9.3 Index]