run_allele_hmm_s3 {hahmmr} | R Documentation |
Run a 3-state allele HMM
Description
Run a 3-state allele HMM
Usage
run_allele_hmm_s3(
pAD,
DP,
R,
p_s,
t = 1e-05,
theta_min = 0.08,
gamma = 20,
r = 0.015
)
Arguments
pAD |
integer vector Paternal allele counts |
DP |
integer vector Total alelle counts |
R |
numeric vector Variant mapping bias direction |
p_s |
numeric vector Phase switch probabilities |
t |
numeric Transition probability between copy number states |
theta_min |
numeric Minimum haplotype frequency deviation threshold |
gamma |
numeric Overdispersion in the allele-specific expression |
Value
character vector Decoded states
[Package hahmmr version 1.0.0 Index]