palmindex: Palm Index

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

Description

This function calculates the immunoglobulin A (IgA) Index as defined in Palm et al. (2014, doi: 10.1016/j.cell.2014.08.006) for a single taxon in a single sample.

Usage

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

Arguments

posabund	Abundance of the bacteria in the IgA positive/high fraction.
negabund	Abundance of the bacteria in the IgA negative/low fraction.
pseudo	Pseudo count added to the abundance of the IgA negative fraction if the bacteria is not in that fraction. 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 Palm index as defined in Palm et al. (2014, doi: 10.1016/j.cell.2014.08.006).

Examples

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

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