assign.autosome.femaleX.cases

autosome.femaleX.trans.probs

DO_autosome_recomb_freq

DO_femaleX_recomb_freq

DO_maleX_recomb_freq

femaleX.trans.probs

maleX.trans.probs

emission_prob_from_r

filter_smooth_allele

filter_smooth_intensity

initialize.hmm

kinship_from_r

strip.quality.columns

tabulate.geno

check.args

convert.pos.to.GRanges

convert.pos.to.bp

viterbi_from_r

internal

internal_functions

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

internal_functions: Internal functions for DOQTL

Description

Arguments