read.ms {hierfstat}

Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs.

Description

With argument what="SNP", each site is read as a SNP, with the ancestral allele encoded as 0 and the alternate allele encoded as 1. If the ms output file contains several replicates, the different replicates will be collated together. Hence, the number of loci is the sum of all sites from all replicates.

Usage

read.ms(fname,what=c("SNP","Haplotype"))

Arguments

fname

file name containing ms output

what

whether to read ms output as SNPs or haplotypes

Details

With argument what="Haplotype", each different sequence from a replicate is read as a haplotype, by converting it first to a factor, and then to an integer. There will be as many loci as there are replicates, and the number of alleles per locus will be the number of different haplotypes in the corresponding replicate.

Value

alldat a data frame with nloc+1 columns, the first being the population to which the individual belongs and the next being the genotypes, one column per locus; and one row per (haploid) individual.

Author(s)

Jerome Goudet [e-mail]

References

Hudson, R. R. (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18 : 337-338.

Examples

## Not run: 
  datH<-read.ms(system.file("extdata","2pops_asspop.txt",package="hierfstat"),what="Haplotype")
  dim(datH)
  head(datH[,1:10]
  datS<-read.ms(system.file("extdata","2pops_asspop.txt",package="hierfstat"),what="SNP")
  dim(datS)
  head(datS[,1:10])
  
## End(Not run)