effectsArray2list: Converts an array of posterior samples of multi-trait marker...

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Converts an array of posterior samples of multi-trait marker effects to a named list (one for each trait).

Description

Converts an array of posterior samples of multi-trait marker effects to a named list (one for each trait).

Usage

effectsArray2list(effectsArray, snpIDs, traits, nIter, burnIn, thin)

Arguments

effectsArray	According to BGLR documentation: 3D array, with dim=c(nRow,p,traits), where nRow number of MCMC samples saved, p is the number of predictors and traits is the number of traits. Multitraitwrites a binary file to disk when saveEffects=TRUE is specified. It can be read to R with readBinMatMultitrait.
snpIDs	character vector with labels for the predictors (SNPs), numeric should work too, but untested.
traits	character vector to label the traits.
nIter	number of iterations used for MCMC; used internally only to exclude burn-in samples from computation
burnIn	burnIn for MCMC; used internally only to exclude burn-in samples from computation
thin	thin for MCMC; used internally only to exclude burn-in samples from computation

Value

list of matrices, one matrix per trait, each matrix has nrow((nIter-burnIn)/thin) and ncol(length(snpIDs)). Each element of the list is named with a string identifying the trait and the colnames of each matrix are labelled with snpIDs.

See Also

Other helper: backsolveSNPeff(), centerDosage(), crosses2predict(), dose2domDevGenotypic(), dose2domDev(), genmap2recombfreq(), genoVarCovarMatFunc(), getAF(), getMAF(), getPropHom(), intensity(), kinship(), maf_filter(), quadform(), remove_invariant()

Other helper: backsolveSNPeff(), centerDosage(), crosses2predict(), dose2domDevGenotypic(), dose2domDev(), genmap2recombfreq(), genoVarCovarMatFunc(), getAF(), getMAF(), getPropHom(), intensity(), kinship(), maf_filter(), quadform(), remove_invariant()

wolfemd/genomicMateSelectR documentation built on July 1, 2022, 10:42 p.m.