MIMOSA: Fit a MIMOSA Model

In MIMOSA: Mixture Models for Single-Cell Assays

Description

This method fits a MIMOSA model to count data stored in an ExpressionSet object.

Usage

MIMOSA(formula, data, ...)

Arguments

formula	describing the features on the lhs and the phenodata on the rhs, supporting extended formula interface with conditioning.
data	an ExpressionSet object with features on rows and samples (labelled with phenoData) on columns.
...	additional arguments

Details

The ExpressionSet should be fully annotated with featureData and phenoData. For ICS data, for example, features would be positive and negative counts for different cytokine producing cell subsets (i.e. IFNg_pos, IFNg_neg) The formula lhs should contain features and the rhs should contain phenotypic variable. See the vignette for an example.

Value

an object of type MIMOSAResult

See Also

MIMOSA-package ConstructMIMOSAExpressionSet MIMOSAResult

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')

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’:

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