R: Find whether snps are in the given regions.

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

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]