Read.PyRAD.Alleles.2: Read.PyRAD.Alleles.2.R Function to read the alignments of a...
In radamsRHA/Misc.Statistics.Genetics.Models:

Description Usage Arguments Examples

View source: R/Read.PyRAD.Alleles.2.R

The function returns a list of alignments obtained from a *.alleles file generated by pyRAD

1	Read.PyRAD.Alleles.2(alleles.file, popID)

`alleles.file`	*.alleles file that is generated by pyRAD
`popID`	vector containing all of the samples ID that are extracted from the alignments

library(AlnStats)
library(stringr)

EXAMPLE
wanted <- c(">CV0031_0", ">CV0031_1", ">CV0310_0",">CV0310_1")
aln.data <- read.alleles2(alleles.file = '~/Desktop/EXAMPLE.alleles', popID = wanted)
S.data <- Calc.S(alleles.data = aln.data)
hist(S.data$theta.hat.vec)
hist(S.data$S.vec)