rhaplo: Generation of Random Haplotype Matrix
In miraculix: Algebraic and Statistical Functions for Genetics

Description Usage Arguments Value See Also Examples

A random haplotype matrix is generated according to some given frequencies.

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rhaplo(freq, indiv, loci, freq2, file,
       file.type = c("beagle", "plink", "plink2"),
       debugging = FALSE)

`freq`	vector of probabilities which gives the allele frequencies for one or both haplotypes; if not given, a half is assumed and `loci` must be given.
`indiv`	number of individuals
`loci`	if not given, the number of loci equals the length of `freq`, otherwise `freq` is recycled to reach the given nnumber of loci
`freq2`	optional. Frequencies for the second chromosome. The vector `freq2` may have a different length than `freq` if `loci` is given or `freq2` is a scalar. The vector `freq2` may contain `NA`s. Then, the value of the second chromosome at this locus is taken over from the first chromosome.
`file, file.type`	string. If given, a file is written that mimics the `file.type` style. An extension is appended to `file` according to the `file.type` style.
`debugging`	logical. Mainly for internal purposes. If `TRUE` the genomic matrix is appended as an attribute to the return value.

If missing(file) an object of class genomicmatrix is returned, else the file name with appended extension according to file.type

A haplotype file can be read in by genomicmatrix.

as.matrix transforms a genomicmatrix to a human readable matrix.

 

as.matrix(rhaplo(seq(0, 1, len=10), indiv=5))

## note that the next examples write a file on the current directory
file <- "miraculix"
if (interactive() && !file.exists(paste0(file, ".bgl"))) {
  f <- rhaplo(freq = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6),
              freq2 = c(0.6, 0.4, 0.5, 0.3, 0.0, 1.0),
              indiv=5, file=file, file.type="beagle",
              debugging = TRUE)
  print(f)
  print(as.genomicmatrix(f))
  print(g <- genomicmatrix(f))
  print(as.matrix(g))
 
  stopifnot(all(as.matrix(g) == attr(f, "M")))
  file.remove(f)
}