User Constructor for class. Calls VCFData constructor: ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary.

Description

User Constructor for class. Calls VCFData constructor: ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary.

Usage

ReadVCFData(mydir, myfile, genome)

Arguments

Value

Object of class VCFData

Examples

vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
mydir <- paste(dirname(vcffn), "/", sep="")
myfile <-basename(vcffn)
vcf <- ReadVCFData(mydir, myfile, "GRCh38")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(genotypeeval)
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

Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genotypeeval/ReadVCFData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ReadVCFData
> ### Title: User Constructor for class.  Calls VCFData constructor:
> ###   ReadVCFData is a wrapper for readVcfAsVRanges.  It removes indels, GL
> ###   chromosomes, and MULTI calls. It scans the header of the vcf file and
> ###   adds in the following fields for analysis if present: AD, GT, DP, GQ.
> ###   Looks for the "END" tag in the header and reads in file as gVCF if
> ###   necessary.
> ### Aliases: ReadVCFData
> 
> ### ** Examples
> 
> vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
> mydir <- paste(dirname(vcffn), "/", sep="")
> myfile <-basename(vcffn)
> vcf <- ReadVCFData(mydir, myfile, "GRCh38")
Reading VCF ... 
Warning message:
In keepSeqlevels(.Object@vr, reg.chrs) :
  invalid seqlevels'1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', 'X', 'Y'were ignored
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>