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

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

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.

Details

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

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.

Author(s)

Daniel Gatti

See Also

calc.genoprob

Examples

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

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.