readSNPTable {MethylSeekR} | R Documentation |
Loading SNPs from tab-delimited file or saved GRanges object
readSNPTable(FileName, seqLengths, format = "text")
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. |
A GRanges object containing the coordinates of the SNPs.
Lukas Burger lukas.burger@fmi.ch
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)