Description Usage Arguments Value See Also

View source: R/fitZeroLogNormal.R

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.

1 | ```
fitZeroLogNormal(obj, mod, coef = 2, szero = TRUE, spos = TRUE)
``` |

`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. |

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

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