RSNPs: Find whether snps are in the given regions.

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

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)

wzthu/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.