View source: R/outputSomaticVariants.R
writeToVCF | R Documentation |
exports variants to VCF
writeToVCF(q, vcfFile, genome = "hg19", snvOnly = F, addSomaticP = F)
q |
A variant data frame from superFreq. |
vcfFile |
The path to the output file. |
genome |
The genome, such as 'hg19', 'hg38' or 'mm10'. Defaults to 'hg19'. |
addSomaticP |
boolean. Set to TRUE to include a column with the somaticP score from superFreq. Defaults to FALSE. |
SNVonly |
boolean. Set to TRUE to only output SNVs, not indels. Defaults to FALSE. |
This function outputs superFreq variants to a VCF for access from other software.
## Not run:
data = loadData(Rdirectory)
q = data$allVariants$variants$variants$mySample
writeToVCF(q, 'mySample.superFreq.vcf')
## End(Not run)
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