getPlots: Getter for VCFQAReport class to return plots slot.
In jentom/genotypeeval: QA/QC of a gVCF or VCF file
Description
Usage
Arguments
Value
Examples
Description
Getter for VCFQAReport class to return plots slot.
Usage
1
getPlots(Object)
Arguments
Object
Object of Class VCFQAReport
Value
List of named ggplots
Examples
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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)
getPlots(ev)
jentom/genotypeeval documentation built on May 13, 2019, 12:54 p.m.
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Description Usage Arguments Value Examples
Description
Getter for VCFQAReport class to return plots slot.
Usage
1 | getPlots(Object)
|
Arguments
Object |
Object of Class VCFQAReport |
Value
List of named ggplots
Examples
1 2 3 4 5 6 7 8 | 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)
getPlots(ev)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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