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

Description Usage Arguments Value See Also

View source: R/fitZeroLogNormal.R

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

1
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



metagenomeSeq documentation built on May 20, 2017, 9:57 p.m.
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