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/getPlots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPlots
> ### Title: Getter for VCFQAReport class to return plots slot.
> ### Aliases: getPlots
>
> ### ** 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 ...
> getPlots(ev)
$chr
$read_depth
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
$variant_type
$homref
$gq
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
