genotypeeval: QA/QC of a gVCF or VCF file
Version 1.8.0

Takes in a gVCF or VCF and reports metrics to assess quality of calls.

AuthorJennifer Tom [aut, cre]
Bioconductor views BatchEffect DataImport Genetics SNP Sequencing VariantAnnotation
Date of publicationNone
MaintainerJennifer Tom <tom.jennifer@gene.com>
Licensefile LICENSE
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genotypeeval")

Getting started

genotypeeval_vignette

Popular man pages

callbyChrPlot: Dot plot of variant call counts (hom alt and het) by...
chunkData: chunkData is a private function to read in a chunk and...
GoldDataParam-class: Declare class GoldDataParam which will store thresholds to...
meanGQ: Mean Genotype Quality (GQ)
numberOfHets: Count Number of Hets
percentInTarget: percent in target range read depth For 15 to 60 for 30x (50...
reformatData: Take in the results from the population data and re-format it
See all...

All man pages Function index File listing

Man pages

admixture: admixture - estimate admixture components using supervised...
callbyChrPlot: Dot plot of variant call counts (hom alt and het) by...
calltypePlot: Bar plot of variants (counts)
chunkData: chunkData is a private function to read in a chunk and...
computeTiTv: Private function to calc transition tranversion (titv) ratio
didSamplePass: Getter for VCFEvaluate class to check if Sample Passed....
didSamplePassOverall: Getter for VCFEvaluate class to check if Sample Passed....
genotypeQualityPlot: Histogram of genotype qualities
getCoefs: Private function to calc coefficients for admixture
getName: Getter for VCFQAReport class to return filename slot
getPlots: Getter for VCFQAReport class to return plots slot.
getResults: Getter for VCFQAReport class to return results. Return a...
getVR: getVr is a Getter. Returns vr slot.
goldCompare: Comparator to gold standard
GoldData-class: Declare class Gold to store information from Gold" (1000...
GoldDataFromGRanges: User Constructor for class. Used to associate the gold...
GoldDataParam: User Constructor for class
GoldDataParam-class: Declare class GoldDataParam which will store thresholds to...
hetGap: Gap between HETs by Chromosome
hetsMasked: Number hets in masked GRanges
homrefPlot: Dot plot of variant call counts (hom ref) by chromosome
meanGQ: Mean Genotype Quality (GQ)
myf: Private function to calc likelihood for admixture
numberCalls: Total Calls. This is the total number of calls in the file...
numberOfHets: Count Number of Hets
numberOfHomRefs: Count Number of Hom Ref
numberOfHomVars: Count Number of Hom Vars
percentHets: Percent of Hets as Total number of variants
percentInTarget: percent in target range read depth For 15 to 60 for 30x (50...
rareCompare: Comparator to rare variants. Rare is defined as 0.01 percent...
readDepth: Median read depth
readdepthPlot: Histogram of read depth by GT
ReadGoldData: User Constructor for class
ReadVCFData: User Constructor for class. Calls VCFData constructor:...
ReadVCFDataChunk: User Constructor for class. Calls VCFData constructor:...
readVcfGold: Private method for class. Read in Gold file - will read in...
reformatData: Take in the results from the population data and re-format it
titv: Transition transversion ratio in coding and non-coding
VCFData-class: Declare class Reads in VCF using readVCFAsVRanges
VCFEvaluate: Constructor for class. Calls constructor for class. Using...
VCFQAParam: User Constructor for class. Call limits are set as default...
VCFQAParam-class: Declare class VCFQAParam which will store thresholds to apply...
VCFQAReport-class: Declare class VCFQAReport which will evaluate a VCF stored as...

Functions

GoldData-class Man page
GoldDataFromGRanges Man page Source code
GoldDataParam Man page Source code
GoldDataParam-class Man page
ReadGoldData Man page Source code
ReadVCFData Man page Source code
ReadVCFDataChunk Man page Source code
VCFData-class Man page
VCFEvaluate Man page Source code
VCFQAParam Man page Source code
VCFQAParam-class Man page
VCFQAReport-class Man page
admixture Man page
callbyChrPlot Man page
calltypePlot Man page
chunkData Man page Source code
computeTiTv Man page Source code
didSamplePass Man page Source code
didSamplePassOverall Man page Source code
genotypeQualityPlot Man page
getCoefs Man page Source code
getName Man page Source code
getPlots Man page Source code
getResults Man page Source code
getVR Man page Source code
goldCompare Man page
hetGap Man page
hetsMasked Man page
homrefPlot Man page
makeHistogram Source code
meanGQ Man page
myf Man page Source code
numberCalls Man page
numberOfHets Man page
numberOfHomRefs Man page
numberOfHomVars Man page
pcaPlot Source code
percentHets Man page
percentInTarget Man page
rareCompare Man page
readDepth Man page
readVcfGold Man page Source code
readdepthPlot Man page
reformatData Man page Source code
titv Man page
tsnePlot Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/GoldData.R
R/GoldDataParam.R
R/PopulationSummary.R
R/VCFData.R
R/VCFQAParam.R
R/VCFQAReport.R
inst
inst/NEWS.Rd
inst/doc
inst/doc/genotypeeval_vignette.html
inst/ext-data
inst/ext-data/chr22.GRCh38.vcf.gz
inst/ext-data/chr22.GRCh38.vcf.gz.tbi
inst/ext-data/example_gold_file.vcf
man
man/GoldData-class.Rd
man/GoldDataFromGRanges.Rd
man/GoldDataParam-class.Rd
man/GoldDataParam.Rd
man/ReadGoldData.Rd
man/ReadVCFData.Rd
man/ReadVCFDataChunk.Rd
man/VCFData-class.Rd
man/VCFEvaluate.Rd
man/VCFQAParam-class.Rd
man/VCFQAParam.Rd
man/VCFQAReport-class.Rd
man/admixture.Rd
man/callbyChrPlot.Rd
man/calltypePlot.Rd
man/chunkData.Rd
man/computeTiTv.Rd
man/didSamplePass.Rd
man/didSamplePassOverall.Rd
man/genotypeQualityPlot.Rd
man/getCoefs.Rd
man/getName.Rd
man/getPlots.Rd
man/getResults.Rd
man/getVR.Rd
man/goldCompare.Rd
man/hetGap.Rd
man/hetsMasked.Rd
man/homrefPlot.Rd
man/meanGQ.Rd
man/myf.Rd
man/numberCalls.Rd
man/numberOfHets.Rd
man/numberOfHomRefs.Rd
man/numberOfHomVars.Rd
man/percentHets.Rd
man/percentInTarget.Rd
man/rareCompare.Rd
man/readDepth.Rd
man/readVcfGold.Rd
man/readdepthPlot.Rd
man/reformatData.Rd
man/titv.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/testQA.R
vignettes
vignettes/genotypeeval_vignette.Rmd
vignettes/my.bib
genotypeeval documentation built on May 20, 2017, 10:04 p.m.

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