how to calculate Polymorphic Informative Content (PIC) from a VCF file
Previously I've seen that other publications have used PowerMarker software to calculate Polymorphic Informative Content (PIC) for loci SNPs in a VCF file. However, this is outdated software (circa 2006), running only on an old version of Windows. Is there a function from a package in R that can calculate it... or a hint at how to manually perform it? Other software?
The formula from the original publication returns a scalar or a vector? I am expecting a vector or in other words a PIC value per loci.
my hack at doing it manually, where a2 is the frequency of allele 2.
var_freq$PIC_a2 <- (1-(var_freq$a2^2)-(1-var_freq$a2)^2)-(2*(var_freq$a2^2)*(1-(var_freq$a2^2))))
Is that right?
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