Constructor for class. Calls constructor for class. Using the GENO fields present in the vcf header will evaluate the vcf file using metrics and generate plots. Each metric will be tested against the params specified in the params class. For example, if Read Depth is in the GENO header will calculate median read depth, percent in target (50 percent to 200 percent of the target specified in the params file) and generate a histogram of Read Depth.

Description

Constructor for class. Calls constructor for class. Using the GENO fields present in the vcf header will evaluate the vcf file using metrics and generate plots. Each metric will be tested against the params specified in the params class. For example, if Read Depth is in the GENO header will calculate median read depth, percent in target (50 percent to 200 percent of the target specified in the params file) and generate a histogram of Read Depth.

Usage

VCFEvaluate(myvcf, vcfparams, gold.ref = NA, cds.ref = NA,
  masked.ref = NA, admixture.ref = NA)

Arguments

Value

Object of VCFQAReport.

Examples

vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
mydir <- paste(dirname(vcffn), "/", sep="")
myfile <-basename(vcffn)
svp <- ScanVcfParam(which=GRanges("22", IRanges(0,200e5)), geno="GT")
vcfparams <- VCFQAParam(count.limits=c(3014580000, Inf), readdepth.target = 30)
vcf <- ReadVCFData(mydir, myfile, "GRCh38")
ev <- VCFEvaluate(vcf, vcfparams)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/VCFEvaluate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: VCFEvaluate
> ### Title: Constructor for class.  Calls constructor for class.  Using the
> ###   GENO fields present in the vcf header will evaluate the vcf file
> ###   using metrics and generate plots.  Each metric will be tested against
> ###   the params specified in the params class.  For example, if Read Depth
> ###   is in the GENO header will calculate median read depth, percent in
> ###   target (50 percent to 200 percent of the target specified in the
> ###   params file) and generate a histogram of Read Depth.
> ### Aliases: VCFEvaluate
> 
> ### ** Examples
> 
> vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
> mydir <- paste(dirname(vcffn), "/", sep="")
> myfile <-basename(vcffn)
> svp <- ScanVcfParam(which=GRanges("22", IRanges(0,200e5)), geno="GT")
> vcfparams <- VCFQAParam(count.limits=c(3014580000, Inf), readdepth.target = 30)
> 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
> ev <- VCFEvaluate(vcf, vcfparams)
 Evaluating File ...  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>