run_glm

Fits a binomial generalized linear model to test for differential
proportions between conditions for a single transcript.

internal

A compositional statistical framework for absolute proportion
estimation between fractions in RNA sequencing data. 'FracFixR' addresses
the fundamental challenge in fractionated RNA-seq experiments where library
preparation and sequencing depth obscure the original proportions of RNA
fractions. It reconstructs original fraction proportions using non-negative
linear regression, estimates the "lost" unrecoverable fraction, corrects
individual transcript frequencies, and performs differential proportion
testing between conditions. Supports any RNA fractionation protocol including
polysome profiling, sub-cellular localization, and RNA-protein complex isolation.

Alice Cleynen

FracFixR

Compositional Statistical Framework for RNA Fractionation
Analysis

Agin Ravindran

Nikolay Shirokikh

run_glm function

<dl><dt>transcript</dt>
<dd>Transcript identifier</dd>
<dt>counts</dt>
<dd>Total count matrix</dd>
<dt>successes</dt>
<dd>Proportion matrix</dd>
<dt>sample_info</dt>
<dd>Sample metadata with Condition factor</dd></dl>

Arguments

run_glm: Binomial GLM for Single Transcript — run_glm

<dl>

<dt>transcript</dt>
<dd>Transcript identifier</dd>


<dt>counts</dt>
<dd>Total count matrix</dd>


<dt>successes</dt>
<dd>Proportion matrix</dd>


<dt>sample_info</dt>
<dd>Sample metadata with Condition factor</dd>

</dl>

run_glm: run_glm: Binomial GLM for Single Transcript

Description

Usage

Value

Arguments