HeatmapRankings: Heatmap of genes and rankings

In GeneSelector: Stability and Aggregation of ranked gene lists

Description

Cluster genes and repeated rankings simultaneously based on a data matrix of ranks whose columns correspond to rankings and whose rows correspond to genes. The main goal is to compare different ranking procedures and to examine whether there are differences among them. Up to now, the Euclidean metric and complete-linkage clustering is used to generate the trees.

Usage

HeatmapRankings(RR, ind=1:100)

Arguments

RR	An object of class RepeatedRanking, usually generated from a call to MergeMethods.
ind	A vector of gene indices whose ranks are used to generate the heatmap. The number of elements should not be too large (not greater than 500) due to high time- and memory requirements.

Value

A heatmap (plot).

Author(s)

Martin Slawski
Anne-Laure Boulesteix

References

Gentleman, R., Carey, V.J., Huber, W., Irizarry, R.A., Dudoit, S. (editors), 2005.
Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Chapter 10: Visualizing Data. Springer, N.Y.

Examples

## Load toy gene expression data
data(toydata)
### class labels
yy <- toydata[1,]
### gene expression
xx <- toydata[-1,]
### Get Rankings from five different statistics
ordinaryT <- RankingTstat(xx, yy, type="unpaired")
baldilongT <- RankingBaldiLong(xx, yy, type="unpaired")
samT <- RankingSam(xx, yy, type="unpaired")
wilc <- RankingWilcoxon(xx, yy, type="unpaired")
wilcebam <- RankingWilcEbam(xx, yy, type="unpaired")
merged <- MergeMethods(list(ordinaryT, baldilongT, samT, wilc, wilcebam))
### plot the heatmap
HeatmapRankings(merged, ind=1:100)

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, 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

Welcome to Bioconductor

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


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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GeneSelector documentation built on May 1, 2019, 11:35 p.m.