Write IBD probabilities to file. — writeIBDs • statgenIBD

Writes IBD probabilities to a plain text, tab-delimited .txt or .ibd file. Information about the file format can be found in the vignette ( vignette("IBDFileFormat", package = "statgenIBD")).

Usage

writeIBDs(IBDprob, outFile, decimals = 6, minProb = 0, compress = FALSE)

Arguments

IBDprob: An object of class IBDprob containing the IBD probabilities.
outFile: A character string specifying the path of the output file.
decimals: An integer value specifying the number of decimals to include in writing the output file.
minProb: A numerical value between zero and 1 / number of parents, specifying the minimum probability cutoff value. Probabilities below this cutoff are set to zero and other probabilities are rescaled to make sure that the probabilities sum up to one.
compress: Should the output be compressed to .gz format?

Value

No output. The output file is created as a result of calling this function.

Examples

## Compute IBD probabilities for Steptoe Morex.
SxMIBD <- calcIBD(popType = "DH",
                 markerFile = system.file("extdata/SxM", "SxM_geno.txt",
                                         package = "statgenIBD"),
                 mapFile = system.file("extdata/SxM", "SxM_map.txt",
                                      package = "statgenIBD"))

## Write IBDs to temporary files.
writeIBDs(IBDprob = SxMIBD, outFile = tempfile(fileext = ".txt"))

## Write IBDs to file, set values <0.05 to zero and only print 3 decimals.
writeIBDs(IBDprob = SxMIBD, outFile = tempfile(fileext = ".txt"),
         decimals = 3, minProb = 0.05)