readSNPTable {MethylSeekR} | R Documentation

## Load SNP table

### Description

Loading SNPs from tab-delimited file or saved GRanges object

### Usage

    readSNPTable(FileName, seqLengths, format = "text")

### Arguments

`FileName` | File Name.
`seqLengths` | A named vector indicating the chromosome lengths of the genome used.
`format` | File format. If format is set to "text", the argument FileName should refer to a tab-delimited text file in the format: chromosome position, where each line stands for a SNP. If format="GRanges", the file is assumed to be a GRanges object, containing the SNP coordinates, saved in rds format.

### Value

A GRanges object containing the coordinates of the SNPs.

### Author(s)

Lukas Burger lukas.burger@fmi.ch

### Examples

    library(MethylSeekR)

    # get chromosome lengths
    library("BSgenome.Hsapiens.UCSC.hg18")
    sLengths=seqlengths(Hsapiens)

    #read SNP data
    snpFname <- system.file("extdata", "SNVs_hg18_chr22.tab",
    package="MethylSeekR")
    snps.gr <- readSNPTable(FileName=snpFname, seqLengths=sLengths)

[Package MethylSeekR version 1.30.0 Index]