statgenIBD (version 1.0.9)

readRABBIT: Read IBD probabilities

Description

Read a file with IBD probabilities computed by the RABBIT software package, see RABBIT for details. It is possible to additionally read the pedigree file that is also used by RABBIT. Reading this file allows for plotting the pedigree.

Usage

readRABBIT(infile, pedFile = NULL)

Value

An IBDprob object with map and markers corresponding to the imported information in the imported .csv file.

Arguments

infile

A character string, a link to a .csv file with IBD probabilities. Compressed .csv files with extension ".gz" or ".bz2" are supported as well.

pedFile

A character string, a link to a .csv file with pedigree information as used by RABBIT as input. Compressed .csv files with extension ".gz" or ".bz2" are supported as well.

References

Zheng, Chaozhi, Martin P Boer, and Fred A Van Eeuwijk. “Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree.” G3 Genes|Genomes|Genetics 8 (10): 3231–45. https://doi.org/10.1534/G3.118.200340.

Examples

if (FALSE) {
## Read RABBIT data for barley.
genoFile <- system.file("extdata/barley", "barley_magicReconstruct.zip",
                       package = "statgenIBD")
barleyIBD <- readRABBIT(unzip(genoFile, exdir = tempdir()))
}