arp2vcf: Converts fastsimcoal2 simulated DNA data to a vcf format

Description Usage Arguments Value Examples

View source: R/arp2vcf.R

Description

This parses an arlequin formatted output of fastsimcoal2. Then, it converts the file into a vcf. The fastsimcoal2 simulates alleles, this function assembles those alleles into individual using the given ploidy. Individual genotypes are labeled by individual number and population.

Usage

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arp2vcf(filePath = NULL, outFile = NULL, ploidy = 2)

Arguments

filePath

full path and name of the arp file

outFile

full path and name of the desired outfile file

ploidy

ploidy of the organism. Default is 2 (diploid)

Value

A data.table with structure similar to a vcf

Examples

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filePath <- "D:/OneDrive/uniFiles/coalescentSimu/snputility/simuRADseq_2Pop/simuRADseq/simuRADseq_1_1.arp"
ploidy <- 2
x <- arp2vcf(filePath = filePath, ploidy = ploidy)

dinmatias/reconproGS documentation built on Sept. 9, 2017, 12:24 a.m.