statgenIBD (version 1.0.9)

writeIBDs: Write IBD probabilities to file.

Description

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)

Value

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

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?

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)