read.ms.output: A utility function to read ms output

Description

This function reads in the output of the program ms, a program to generate samples under a variety of neutral models.

The argument indicates either a file name or a vector of character strings, one string for each line of the output of ms. As with the second case, it is appropriate with system(,intern=TRUE), see example below.

Usage

read.ms.output(msout,is.file=TRUE,xpose=TRUE,verbose=TRUE,
               outfile=NULL,outfileonly=FALSE)

Arguments

msout

an ms output

is.file

a flag indicating ms output as a system file or an R object

xpose

a flag to obtain the tranposed format as it is (when TRUE)

verbose

when TRUE, display on screen every 1000 for large nsam

outfile

to save the haplotypes in a tab-delimited ASCII file

outfileonly

to reset gametes to NA when nsam/nreps is very large and is useful with outfile

Value

The returned value is a list storing the results.
callsystem call to ms
seedrandom number seed to ms
nsamnumber of copies of the locus in each sample
nrepsthe number of independent samples to generate
segsitesa vector of the numbers of segregating sites
timesvectors of time to most recent ancester (TMRCA) and total tree lengths
positionspositions of polymorphic sites on a scale of (0,1)
gametesa list of haplotype arrays
probsthe probability of the specified number of segregating sites given the genealogical history of the sample and the value to -t option

References

Hudson RR (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8,

Press WH, SA Teukolsky, WT Vetterling, BP Flannery (1992). Numerical Recipes in C. Cambridge University Press, Cambridge.

Examples

Run this code

# Assuming ms is on the path

system("ms 5 4 -s 5 > ms.out")
msout1 <- read.ms.output("ms.out")

system("ms 50 4 -s 5 > ms.out")
msout2 <- read.ms.output("ms.out",outfile="out",outfileonly=TRUE)

msout <- system("ms 5 4 -s 5 -L", intern=TRUE)
msout3 <- read.ms.output(msout,FALSE)