fdr {MIMOSA}R Documentation

Compute the fdr (q-value) from posterior probabilities

Description

Given the z's from a MIMOSA model, calculates the q-values for each observation.

Usage

fdr(z)

## S3 method for class 'matrix'
fdr(z)

## S3 method for class 'MIMOSAResult'
fdr(z)

## S3 method for class 'MIMOSAResultList'
fdr(z)

Arguments

z

matrix of posterior probabilties, or a MIMOSAResult, or MIMOSAResultList

Value

a vector of q-values or a list of vectors of q-values.

Examples

data(ICS)
E<-ConstructMIMOSAExpressionSet(ICS,
                              reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
                               other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
                               default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
                               .variables=.(TCELLSUBSET,CYTOKINE,UID),
                               featureCols=1,ref.append.replace='_REF')
result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
   data=E, method='EM',
   subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
   ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
qvalues<-fdr(result)
[Package MIMOSA version 1.16.1 Index]