Read IBD probabilities

Read a file with IBD probabilities computed by the RABBIT software package. It is possible to additionally read the pedigree file that is also used by RABBIT. Reading this file allows for plotting the pedigree. Phenotypic data can be added from a data.frame.

Usage

readRABBITMPP(infile, pedFile = NULL, pheno = NULL)

Arguments

infile

A character string, a link to a .csv file with IBD probabilities.

pedFile

A character string, a link to a .csv file with pedigree information as used by RABBIT as input.

pheno

A data frame with at least columns "genotype" for the "genotype" and one or more numerical columns containing phenotypic information. A column "cross" can be used for indicating the cross the genotype comes from.

Value

An object of class gDataMPP with map and markers corresponding to the imported information in the imported .csv file.

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

## Read RABBIT data for barley.
genoFile <- system.file("extdata/barley", "barley_magicReconstruct.zip",
                       package = "statgenMPP")
barleyMPMPP <- readRABBITMPP(unzip(genoFile, exdir = tempdir()))