Generate allele frequency table for individuals or populations
Source:R/allele_tests.R
allele.freq.RdGet alternative allele frequency across all individuals per SNP from the genotype or allele depth tables
Usage
allele.freq(gtt, f.typ = c("pop", "ind"), verbose = TRUE)Arguments
- gtt
a list or data frame of genotype and/or allele depth table produced from
hetTgen(or similar)- f.typ
character. type of allele frequency to be calculated (individual
"ind"or population"pop")- verbose
logical. whether to show the progress of the analysis
Details
If the allele frequencies to be calculated for populations from both genotype table and the allele depth table, they must be provided in a list with element names AD for allele depth table and GT for the genotype table. See the examples.
Examples
vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf,"GT")
#> generating table
#>
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ad.table<-hetTgen(vcf,"AD")
#> generating table
#>
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# for individual based AF
frQ<-allele.freq(het.table,f.typ="ind")
#> genotype table provided
#> calculating allele frequency from genotype
#>
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#for population-wise and both allele depth and genotype tables
if (FALSE) frQ<-allele.freq(list(AD=ad.table,GT=het.table),f.typ="pop")