example_annotation

A data frame containing sample annotations for the example_counts matrix.
Describes the experimental design with conditions, fraction types, and replicates.

datasets

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

example_annotation function

A data frame with 12 rows and 4 columns:<dl>
 <dt>Sample</dt>
<dd>Sample identifier matching column names in example_counts</dd> <dt>Condition</dt>
<dd>Experimental condition (Control or Treatment)</dd> <dt>Type</dt>
<dd>Fraction type (Total, Light_Polysome, or Heavy_Polysome)</dd> <dt>Replicate</dt>
<dd>Replicate identifier (Rep1 or Rep2)</dd>
</dl>

Format

Example annotation data frame — example_annotation

A data frame with 12 rows and 4 columns:<dl>
 <dt>Sample</dt>
<dd>Sample identifier matching column names in example_counts</dd>

 <dt>Condition</dt>
<dd>Experimental condition (Control or Treatment)</dd>

 <dt>Type</dt>
<dd>Fraction type (Total, Light_Polysome, or Heavy_Polysome)</dd>

 <dt>Replicate</dt>
<dd>Replicate identifier (Rep1 or Rep2)</dd>


</dl>

example_annotation: Example annotation data frame

Description

Usage

Arguments

Format

Examples