Fit a MIMOSA Model

Description

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

Usage

MIMOSA(formula, data, ...)

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')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MIMOSA)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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

This is package 'modeest' written by P. PONCET.
For a complete list of functions, use 'library(help = "modeest")' or 'help.start()'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MIMOSA/MIMOSA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MIMOSA
> ### Title: Fit a MIMOSA Model
> ### Aliases: MIMOSA MIMOSA,formula,ExpressionSet-method
> 
> ### ** 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')
Warning message:
In .local(formula, data, ...) :
  Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>