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PRIST (version 0.925)

ZlmFit-class: An S4 class to hold the output of a call to zlm

Description

This holds output from a call to zlm.SingleCellAssay. Many methods are defined to operate on it. See below.

Usage

# S4 method for ZlmFit,CoefficientHypothesis
lrTest(object, hypothesis)
# S4 method for ZlmFit,Hypothesis
lrTest(object, hypothesis)
# S4 method for ZlmFit,matrix
lrTest(object, hypothesis)
# S4 method for ZlmFit,CoefficientHypothesis
waldTest(object, hypothesis)
# S4 method for ZlmFit,Hypothesis
waldTest(object, hypothesis)
# S4 method for ZlmFit
coef(object, which, ...)
# S4 method for ZlmFit
vcov(object, which, ...)
# S4 method for ZlmFit
se.coef(object, which, ...)
# S4 method for ZlmFit
summary(object, logFC = TRUE, doLRT = FALSE, ...)

Arguments

object

ZlmFit

hypothesis

call to Hypothesis or CoefficientHypothesis or a matrix giving such contrasts.

which

character vector, one of "C" (continuous) or "D" (discrete) specifying which component should be returned

...

ignored

logFC

If TRUE, calculate log-fold changes, or output from a call to getLogFC.

doLRT

if TRUE, calculate lrTests on each coefficient, or a character vector of such coefficients to consider.

Methods (by generic)

  • lrTest: Returns an array with likelihood-ratio tests on contrasts defined using CoefficientHypothesis().

  • lrTest: Returns an array with likelihood-ratio tests specified by Hypothesis, which is a Hypothesis.

  • lrTest: Returns an array with likelihood-ratio tests specified by Hypothesis, which is a contrast matrix.

  • waldTest: Returns an array with Wald Tests on contrasts defined using CoefficientHypothesis().

  • waldTest: Returns an array with Wald Tests on contrasts defined in Hypothesis()

  • coef: Returns the matrix of coefficients for component which.

  • vcov: Returns an array of variance/covariance matrices for component which.

  • se.coef: Returns a matrix of standard error estimates for coefficients on component which.

  • summary: Returns a data.table summary of fit (invisibly).

Slots

coefC

coefD

matrices of coefficients

vcovC

vcovD

array of variance/covariance matrices for coefficients

LMlike

the LmWrapper object used

sca

the SingleCellAssay object used

deviance

loglik

df.null

df.resid

dispersion

dispersionNoShrink

priorDOF

priorVar

converged

output that may optionally be set by the underlying modeling function

hookOut

a list of length ngenes containing output from a hook function, if zlm was called with one

See Also

zlm.SingleCellAssay