R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/volcanoPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: volcanoPlot
> ### Title: Volcano plot for a MIMOSA model
> ### Aliases: volcanoPlot
>
> ### ** 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.
> volcanoPlot(result,CYTNUM-CYTNUM_REF)
>
>
>
>
>
> dev.off()
null device
1
>