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.
read.ms.output(msout,is.file=TRUE,xpose=TRUE,verbose=TRUE,
outfile=NULL,outfileonly=FALSE)an ms output
a flag indicating ms output as a system file or an R object
a flag to obtain the tranposed format as it is (when TRUE)
when TRUE, display on screen every 1000 for large nsam
to save the haplotypes in a tab-delimited ASCII file
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.
system call to ms
random number seed to ms
number of copies of the locus in each sample
the number of independent samples to generate
a vector of the numbers of segregating sites
vectors of time to most recent ancester (TMRCA) and total tree lengths
positions of polymorphic sites on a scale of (0,1)
a list of haplotype arrays
the probability of the specified number of segregating sites given the genealogical history of the sample and the value to -t option
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.
# 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)
# }
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