Create SNP black list

Description

Function to create a black list of germline SNPs with expected allelic fraction (AF) smaller than 0.5 in diploid genomes.

Usage

createSNPBlacklist(vcf.files, n = min(10, length(vcf.files)), 
    low.af = 0.025, high.af = 0.1, genome = "hg19")

Arguments

Value

A list with elements snp.black.list and segmented. "snp.black.list" is just a list of SNP ids. "segmented" blacklists whole regions.

Author(s)

Markus Riester

Examples

# Assume VCF files of normals (for example obtained by a MuTect artifact
# detection run) are in directory poolofnormals:
mutect.normal.files <- dir("poolofnormals", pattern="vcf$", full.names=TRUE) 

# These files do not exist in our example, so we do not run the function here.
#snp.blacklist <- createSNPBlacklist(mutect.normal.files)

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)

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> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
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: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PureCN/createSNPBlacklist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: createSNPBlacklist
> ### Title: Create SNP black list
> ### Aliases: createSNPBlacklist
> 
> ### ** Examples
> 
> # Assume VCF files of normals (for example obtained by a MuTect artifact
> # detection run) are in directory poolofnormals:
> mutect.normal.files <- dir("poolofnormals", pattern="vcf$", full.names=TRUE) 
> 
> # These files do not exist in our example, so we do not run the function here.
> #snp.blacklist <- createSNPBlacklist(mutect.normal.files)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>