Last data update: 2014.03.03
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genotypeeval
Package: genotypeeval
Title: QA/QC of a gVCF or VCF file
Version: 1.2.2
Authors@R: person('Jennifer', 'Tom', email = 'tom.jennifer@gene.com',
role=c('aut', 'cre'))
Description: Takes in a gVCF or VCF and reports metrics to assess
quality of calls.
Depends: R (>= 3.2.0), VariantAnnotation
Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges,
GenomeInfoDb, IRanges, methods, BiocParallel
Collate: GoldDataParam.R GoldData.R VCFData.R VCFQAParam.R
VCFQAReport.R PopulationSummary.R
License: file LICENSE
LazyData: true
Suggests: knitr, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene
VignetteBuilder: knitr
Author: Jennifer Tom [aut, cre]
Maintainer: Jennifer Tom <tom.jennifer@gene.com>
biocViews: Genetics, BatchEffect, Sequencing, SNP, VariantAnnotation,
DataImport
NeedsCompilation: no
Packaged: 2016-05-16 05:33:41 UTC; biocbuild
● BiocViews: BatchEffect, DataImport, Genetics, SNP, Sequencing, VariantAnnotation
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5 images,
43 functions,
0 datasets
●
Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'genotypeeval' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval'
** help
*** installing help indices
converting help for package 'genotypeeval'
finding HTML links ... done
GoldData-class html
GoldDataFromGRanges html
GoldDataParam-class html
GoldDataParam html
ReadGoldData html
ReadVCFData html
ReadVCFDataChunk html
VCFData-class html
VCFEvaluate html
VCFQAParam-class html
VCFQAParam html
VCFQAReport-class html
admixture html
callbyChrPlot html
calltypePlot html
chunkData html
computeTiTv html
didSamplePass html
didSamplePassOverall html
genotypeQualityPlot html
getCoefs html
getName html
getPlots html
getResults html
getVR html
goldCompare html
hetGap html
hetsMasked html
homrefPlot html
meanGQ html
myf html
numberCalls html
numberOfHets html
numberOfHomRefs html
numberOfHomVars html
percentHets html
percentInTarget html
rareCompare html
readDepth html
readVcfGold html
readdepthPlot html
reformatData html
titv html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval'
* DONE (genotypeeval)
Making 'packages.html' ... done
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