build_hmm: Build a model to assign haplotypes to each gamete

View source: R/build_hmm.R

build_hmmR Documentation

Build a model to assign haplotypes to each gamete

Description

This function builds a hidden Markov model that considers sequencing error. Uses the HMM packages.

Usage

build_hmm(num_snps, sequencing_error, avg_recomb)

Arguments

num_snps

number of SNPs, found previously from taking the number of rows in the input data. Used to set the denominator for transition probability

sequencing_error

User-input for expected error in sequencing (default = 0.005)

avg_recomb

User-input for expected average recombination spots per chromosome (default=1). Used to set the numerator for transition probability

Value

hmm The hidden Markov model with transition and emission probabilities set for use.


mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.