kauindex: Kau Index

In IgAScores: Score Taxon-Level IgA Binding in IgA-Seq Experiments

Description

This function calculates the immunoglobulin A (IgA) Index as defined in Kau et al. (2015, doi: 10.1126/scitranslmed.aaa4877) for a single taxon in a single sample.

Usage

kauindex(posabund, negabund, pseudo = 1e-05, nazeros = TRUE)

Arguments

posabund	The abundance of the bacteria in the IgA positive/high fraction (abundances should sum to 1 not as a %).
negabund	The abundance of the bacteria in the IgA negative/low fraction (abundances should sum to 1 not as a %).
pseudo	Pseudo count added to both the IgA positive and negative fraction values prior to calculation. Defaults to 1e-5. Recommend setting to minimum observed abundance in whole dataset.
nazeros	Return NA if the pos and neg abundances are both zero. Default is TRUE.

Value

A numeric value for the Kau index as defined in Kau et al. (2015, doi: 10.1126/scitranslmed.aaa4877).

Examples

kauindex(posabund=0.1,negabund=0.2,pseudo=0.0002)

IgAScores documentation built on Sept. 1, 2020, 9:08 a.m.