VennMapper: Wrapper function for VennMapping

In MAMA: Meta-Analysis of MicroArray

Description

This is a wrapper function for meta-analysis using VennMapping method. It performs all necessary steps and provides all available outputs.

Usage

VennMapper(data, varname, cutoff)

Arguments

data	MetaArray object
varname	Character String - name of one column in clinical data matrices to be used as class labels
cutoff	Numeric - cutoff for selection of genes according to their fold-change in log2-scale. e.g. 1 equals to two-fold expression change

Value

An object of class VennMapper.res containing

conting.tab	A contingency table with numbers of overlapping genes in pairs of the datasets
z.score	A table of z-scores describing the significance of overlap in pairs of the datasets
genes	A table of gene names that overlap in pairs of the datasets

Author(s)

Ivana Ihnatova

References

Smid, M., Dorssers, L. C. J. and Jenster, G. 2003, Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes, Bioinformatics, vol. 19 no. 16 2003

Examples

data(ColonData)
vm<-VennMapper(ColonData, "MSI", 1)

Example output

Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

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

    rowVars

Loading required package: xtable
Loading required package: multtest
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, 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")'.

Loading required package: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

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

    multExpFDR, zScoreFDR, zScorePermuted, zScores

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.