runNormalization: Get Per-Feature Theta

In tpq/propr: An R package to calculate proportionality and other measures for compositional data

Get Per-Feature Theta

Description

This function calculates the differential proportionality between each feature and a set of normalization factors. When the normalization factors correctly remove the compositional bias, the resultant thetas indicate differential expression (DE). However, unlike other DE tests, the p-value for differential proportionality is not linked to the normalization factors. Here, normalization factors only affect the interpretation, not the statistics.

Usage

runNormalization(object, norm.factors)

Arguments

object	A propd object.
norm.factors	A numeric vector. The effective library size normalization factors (e.g., from edgeR or DESeq2).

Value

A numeric vector. A theta for each feature.

tpq/propr documentation built on April 21, 2024, 12:50 p.m.