R: A utility function to read ms output

read.ms.output {gap} | R Documentation

## 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.

### 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. 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

### Details

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.

### Author(s)

D Davison, RR Hudson, JH Zhao

### 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

    ## 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)

[Package gap version 1.2.3-6 Index]