Learn R Programming
metagenomeSeq (version 1.14.0)

fitZeroLogNormal: Compute the log fold-change estimates for the zero-inflated log-normal model

Description

Run the zero-inflated log-normal model given a MRexperiment object and model matrix. Not for the average user, assumes structure of the model matrix.

Usage

fitZeroLogNormal(obj, mod, coef = 2, szero = TRUE, spos = TRUE)

Arguments

obj
A MRexperiment object with count data.
mod
The model for the count distribution.
coef
Coefficient of interest to grab log fold-changes.
szero
TRUE/FALSE, shrink zero component parameters.
spos
TRUE/FALSE, shrink positive component parameters.

Value

A list of objects including:
  • logFC - the log fold-change estimates
  • adjFactor - the adjustment factor based on the zero component
  • se - standard error estimates
  • fitln - parameters from the log-normal fit
  • fitzero - parameters from the logistic fit
  • zeroRidge - output from the ridge regression
  • posRidge - output from the ridge regression
  • tauPos - estimated tau^2 for positive component
  • tauZero - estimated tau^2 for zero component
  • exclude - features to exclude for various reasons, e.g. all zeros
  • zeroExclude - features to exclude for various reasons, e.g. all zeros

See Also

cumNorm fitFeatureModel