fdr: Compute the fdr (q-value) from posterior probabilities

In MIMOSA: Mixture Models for Single-Cell Assays

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)

Example output

Loading required package: MASS
Loading required package: plyr
Loading required package: reshape

Attaching package: 'reshape'

The following objects are masked from 'package:plyr':

    rename, round_any

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Warning message:
In .local(formula, data, ...) :
  Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.

MIMOSA documentation built on Nov. 12, 2020, 2:02 a.m.