Starting from a reshaped data frame in the correct format, construct
an ExpressionSet object that can be used with MIMOSA.
Usage
MIMOSAExpressionSet(df, featureCols)
Arguments
df
a data.frame that is in the correct form
featureCols
the indices of the columns that identify features.
Details
The featureCols will be used to construct feature names, and these
columns will be dropped from the exprs matrix. The column names are assumed
to have names that contain '_' characters separating phenotypic
characteristics. These would be generated automatically
if the data frame was constrcuted with 'reshape'. They
are used to construct the phenoData for the expression set
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 'demo()' for some demos, 'help()' for on-line help, or
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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/MIMOSAExpressionSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MIMOSAExpressionSet
> ### Title: Construct an ExpressionSet for MIMOSA
> ### Aliases: MIMOSAExpressionSet
>
> ### ** Examples
>
> 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')
>
>
>
>
>
> dev.off()
null device
1
>