gap: read.ms.output – R documentation

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gap

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.

`call`	system call to ms
`seed`	random number seed to ms
`nsam`	number of copies of the locus in each sample
`nreps`	the number of independent samples to generate
`segsites`	a vector of the numbers of segregating sites
`times`	vectors of time to most recent ancester (TMRCA) and total tree lengths
`positions`	positions of polymorphic sites on a scale of (0,1)
`gametes`	a list of haplotype arrays
`probs`	the 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.

Author(s)

D Davison, RR Hudson, JH Zhao

Examples

## Not run: 

# 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)

## End(Not run)

gap

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21