igaprobabilityratio {IgAScores}

IgA Probability Ratio

Description

Calculate the IgA Probability Ratio score as described in Jackson et al. (2020, doi: 10.1101/2020.08.19.257501).

Usage

igaprobabilityratio(
  posabund,
  negabund,
  possize,
  negsize,
  pseudo = 1e-05,
  scaleratio = TRUE,
  nazeros = TRUE
)

Arguments

posabund

Abundance of the bacteria in the IgA positive/high fraction (abundances should sum to 1 not as a %).

negabund

Abundance of the bacteria in the IgA negative/low fraction (abundances should sum to 1 not as a %).

possize

The fraction of events in the flow cytometer classed as IgA positive/high (as a decimal fraction not a %).

negsize

The fraction of events in the flow cytometer classed as IgA negative/low (as a decimal fraction not a %).

pseudo

Pseudo count added to both the IgA positive and negative abundance values prior to calculation. Defaults to 1e-5. Recommend setting to minimum observed abundance in whole dataset.

scaleratio

Should probratio scores be scaled to the pseudo count. Default is TRUE.

nazeros

Return NA if the pos and neg abundances are both zero. Default is TRUE.

Details

This function calculates the ratio of the immunoglobulin A (IgA) positive fraction probability relative to the IgA negative fraction probability for a single taxa in a single sample. These probabilities can individually be calculated using the igaprobability() function. As both calculations have the whole fraction taxon abundance as a denominator it cancels. This means the IgA probability ratio can be calculated without this information. Further details can be found in Jackson et al. (2020, doi: 10.1101/2020.08.19.257501).

Value

A numeric value for the IgA Probability Ratio as defined in Jackson et al. (2020, doi: 10.1101/2020.08.19.257501).

Examples

igaprobabilityratio(posabund=0.2,negabund=0.05,possize=0.05,negsize=0.6,pseudo=0.0002)