merge2ExpressionSets: Merge two ExpressionSet-objects into one ExpressionSet-object

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

Merge two ExpressionSet-objects into one ExpressionSet-object

Usage

merge2ExpressionSets(GEdata1, GEdata2, verbose=TRUE)

Arguments

GEdata1	Object of class ExpressionSet.
GEdata2	Object of class ExpressionSet.
verbose	Logical indicator: should intermediate output be printed on the screen?

Details

Data of the two objects is assumed to originate from the same samples, and are presented in the same order.

Only the experimental data and annotation information is inherited by the merged object.

Value

Object of class ExpressionSet, restricted to the specified subset of features.

Author(s)

Wessel N. van Wieringen: [e-mail]

References

Van de Wiel, M.A., Kim, K.I., Vosse, S.J., Van Wieringen, W.N., Wilting, S.M. , Ylstra, B. (2007), "CGHcall: an algorithm for calling aberrations for multiple array CGH tumor profiles", Bioinformatics, 23, 892-894.

Van Wieringen, W.N., Unger, K., Leday, G.G.R., Krijgsman, O., De Menezes, R.X., Ylstra, B., Van de Wiel, M.A. (2012), "Matching of array CGH and gene expression microarray features for the purpose of integrative analysis", BMC Bioinformatics, 13:80.

See Also

ExpressionSet.

Examples

# load data
data(pollackGE16) 

# create two cghCall-objects
ids1 <- sample(1:dim(pollackGE16)[1], 10) 
GEdata1 <- pollackGE16[ids1,] 
GEdata2 <- pollackGE16[-ids1,] 

# order the copy number data genomically
pollackGE16 <- merge2ExpressionSets(GEdata1, GEdata2) 

Example output

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: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: mvtnorm
perform input checks... 

sigaR documentation built on April 28, 2020, 6:05 p.m.