ProcessReplicate

This function implements the mathematical core of FracFixR: fitting a
non-negative least squares (NNLS) regression to estimate fraction weights
and correct individual transcript abundances.

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

ProcessReplicate function

<dl><dt>RepMat</dt>
<dd>Data frame with transcripts as rows, samples as columns.
Must include a "Total" column representing the whole cell lysate</dd>
<dt>transcriptlist</dt>
<dd>Character vector of transcript IDs to use for regression.
These should be informative transcripts in the appropriate abundance range</dd></dl>

Arguments

ProcessReplicate: Core NNLS Regression for Individual Replicates — ProcessReplicate

<dl>

<dt>RepMat</dt>
<dd>Data frame with transcripts as rows, samples as columns.
Must include a "Total" column representing the whole cell lysate</dd>


<dt>transcriptlist</dt>
<dd>Character vector of transcript IDs to use for regression.
These should be informative transcripts in the appropriate abundance range</dd>

</dl>

ProcessReplicate: ProcessReplicate: Core NNLS Regression for Individual Replicates

Description

Usage

Value

Arguments

Details