extract_condition_matrix

Extracts count and proportion data for specified conditions and fraction types.
Handles both single fraction and combined fraction analyses.

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

extract_condition_matrix function

<dl><dt>originalcounts</dt>
<dd>Original count matrix</dd>
<dt>proportions</dt>
<dd>Proportion estimates from FracFixR</dd>
<dt>annotation</dt>
<dd>Sample annotation data frame</dd>
<dt>conditions</dt>
<dd>Vector of conditions to extract</dd>
<dt>types</dt>
<dd>Vector of fraction types to analyze</dd></dl>

Arguments

extract_condition_matrix: Extract and Prepare Data for Statistical Testing — extract_condition_matrix

<dl>

<dt>originalcounts</dt>
<dd>Original count matrix</dd>


<dt>proportions</dt>
<dd>Proportion estimates from FracFixR</dd>


<dt>annotation</dt>
<dd>Sample annotation data frame</dd>


<dt>conditions</dt>
<dd>Vector of conditions to extract</dd>


<dt>types</dt>
<dd>Vector of fraction types to analyze</dd>

</dl>

extract_condition_matrix: extract_condition_matrix: Extract and Prepare Data for Statistical Testing

Description

Usage

Value

Arguments