GOmnplot: A function to plot by group means against each other.

In annotate: Annotation for microarrays

Description

For a two sample comparison, as determined by group, and a specified KEGG pathway or GO category, per group means are computed and plotted against each other.

Usage

GOmnplot(x, eset, data = "hgu133plus2", group, ...)
KEGGmnplot(x, eset, data = "hgu133plus2", group, ...)

Arguments

x	The name of the KEGG pathway or GO category.
eset	An ExpressionSet containing the data.
data	The name of the chip that was used to provide the data.
group	The variable indicating group membership, should have two different values.
...	Extra parameters to pass to the call to plot.

Details

All probes in eset that map to the given category are determined. Then per group, per probe means are computed and plotted against each other. Extra parameters can be passed to the plot function via the dots argument.

Value

The matrix of per group means, for each probe.

Author(s)

R. Gentleman

See Also

KEGG2heatmap

Examples

  library("hgu95av2.db")
  data(sample.ExpressionSet)
  KEGGmnplot("04810", sample.ExpressionSet, sample.ExpressionSet$sex, 
             data = "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


       AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_3_st AFFX-HSAC07/X00351_5_at
Female                4760.580                123.4877                3566.973
Male                  4949.658                110.3674                3472.315
       AFFX-HSAC07/X00351_5_st AFFX-HSAC07/X00351_M_at AFFX-HSAC07/X00351_M_st
Female                177.1625                4355.943                196.4948
Male                  183.6415                4257.735                198.4687
       31719_at 31720_s_at 31699_at 31557_at
Female 1659.094   1655.935 238.9623 5769.618
Male   1456.260   1488.698 245.2747 5851.949

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