Generate shared variation dataset from multiple VCF files

Description

Load multiple vcf files and output a GRange object with SNVs present in multiple samples.

Usage

  Multiple_VCF(vcfs, share_num, ...)

Arguments

Details

This function allows to limit SNVs that are present in at least m out of n VCF files.

Value

a GRange object that contains the shared variations

Author(s)

Xiaojing Wang

Examples

path <- system.file("extdata/vcfs", package="customProDB")
vcfFiles<- paste(path, '/', list.files(path, pattern="*vcf$"), sep='')
vcfs <- lapply(vcfFiles, function(x) InputVcf(x))
shared <- Multiple_VCF(vcfs, share_num=2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(customProDB)
Loading required package: IRanges
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: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/customProDB/Multiple_VCF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Multiple_VCF
> ### Title: Generate shared variation dataset from multiple VCF files
> ### Aliases: Multiple_VCF
> 
> ### ** Examples
> 
> path <- system.file("extdata/vcfs", package="customProDB")
> vcfFiles<- paste(path, '/', list.files(path, pattern="*vcf$"), sep='')
> vcfs <- lapply(vcfFiles, function(x) InputVcf(x))
> shared <- Multiple_VCF(vcfs, share_num=2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>