Load SNP table

Description

Loading SNPs from tab-delimited file or saved GRanges object

Usage

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

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MethylSeekR)
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: mhsmm
Loading required package: mvtnorm
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethylSeekR/readSNPTable.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readSNPTable
> ### Title: Load SNP table
> ### Aliases: readSNPTable
> 
> ### ** Examples
> 
> 
> library(MethylSeekR)
> 
> # get chromosome lengths
> library("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
> sLengths=seqlengths(Hsapiens)
> 
> #read SNP data
> snpFname <- system.file("extdata", "SNVs_hg18_chr22.tab",
+ package="MethylSeekR")
> snps.gr <- readSNPTable(FileName=snpFname, seqLengths=sLengths)
reading SNP table
Read 11750 records
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>