createGSEAFiles: A Wrapper Function to create *.GCT and *.CLS for GSEA...

In ArrayTools: geneChip Analysis Package

Description

A Wrapper Function to create *.GCT and *.CLS for GSEA analysis

Usage

createGSEAFiles(mydir = getwd(), eSet, catVar)

Arguments

mydir	directory where you would like to store the files
eSet	an ExpressionSet
catVar	variable of interest

Value

Creating *.GCT and *.CLS for GSEA

Author(s)

Xiwei Wu, Arthur Li

References

http://www.broad.mit.edu/gsea/

See Also

output.cls, output.gct

Examples

data(eSetExample)
## Not run: createGSEAFiles (mydir, eSetExample, "Treatment")

Example output

Loading required package: affy
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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.