GO2heatmap: Compute a heatmap for the specified data, for either a GO...

In annotate: Annotation for microarrays

Description

For a given GO category or KEGG pathway, all probes in the supplied data are mapped to the pathway and a heatmap is produced.

Usage

GO2heatmap(x, eset, data, ...)
KEGG2heatmap(x, eset, data, ...)

Arguments

x	The name of the category or pathway.
eset	An ExpressionSet providing the data.
data	The name of the chip.
...	Additional parameters to pass to heatmap.

Details

For the given pathway or GO category all matching probes are determined, these are used to subset the data and heatmap is invoked on that set of data. Extra parameters can be passed through to heatmap using the ... parameter. The annotation slot of the eset argument is used to determine the appropriate annotation data to use.

Value

The value returned by heatmap is passed back to the user.

Author(s)

R. Gentleman

See Also

heatmap

Examples

  library("hgu95av2.db")
  data(sample.ExpressionSet)
  KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")

Example output

Loading required package: AnnotationDbi
Loading required package: stats4
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")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: org.Hs.eg.db

annotate documentation built on Nov. 8, 2020, 8:14 p.m.