gt_help

call gt helper, get posterior mean, expected gt and sd expected gt across all samples

The method models RNA-seq reads using a mixture of 3 beta-binomial distributions to generate posterior probabilities for genotyping bi-allelic single nucleotide polymorphisms. Elena Vigorito, Anne Barton, Costantino Pitzalis, Myles J. Lewis and Chris Wallace (2023) <doi:10.1093/bioinformatics/btad393> "BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing."

Elena Vigorito

bbmix

Bayesian Model for Genotyping using RNA-Seq

Chris Wallace

gt_help function

<dl><dt>stan_samples</dt>
<dd>matrix with samples extracted from stan fit object, params mu and lambda</dd>
<dt>pop</dt>
<dd>population to select AF for GT prior, defaults to EUR</dd>
<dt>data</dt>
<dd>data table 1 row with counts and EAF to apply model</dd></dl>

Arguments

call gt helper, get posterior mean, expected gt and sd expected gt across all samples — gt_help

<dl>

<dt>stan_samples</dt>
<dd>matrix with samples extracted from stan fit object, params mu and lambda</dd>


<dt>pop</dt>
<dd>population to select AF for GT prior, defaults to EUR</dd>


<dt>data</dt>
<dd>data table 1 row with counts and EAF to apply model</dd>

</dl>

gt_help: call gt helper, get posterior mean, expected gt and sd expected gt across all samples

Description

Usage

Value

Arguments