condense.model.probs: Condense 36 state genotypes down to founder genotypes.

Description

Additive condenses the heterozygous genotype calls down to the founder allele contributions. Dominance will eventually provide additive and dominance values (method currently uncertain). FALSEull simply gathers all of the genotype probabilities together.

Usage

condense.model.probs(path = ".", write, model = c("additive", "dominance", "full"), cross = "DO") get.additive(files, samples) get.dominance(files, samples) get.full(files, samples)

Arguments

path

Character containing the path to the *.Rdata files that contain the genotype probabilities.

write

Character that is the filename to write the results to.

model

Character string that is one of "additive", "dominance" or "full". See details.

cross

Character string containing the type of cross. Typically "DO, "CC", "HS" or "DOF1". This is used in downsteam analyses to produce the coefficient plots and select strains for association mapping.

files

Vector of files to read.

samples

Character vector of sample IDs that match the files argument.

Value

Three dimensional array of haplotype or genotype probabilities. Num. samples by num. founders (or genotypes) by num. SNPs. Writes out to a *.Rdata file.

Details

get.additive, get.dominance and get.full are helper functions.

Examples

Run this code

  ## Not run:  condense.model.probs(write = "model.probs.Rdata")