affy (version 1.50.0)

runRomer: A function to run the romer function on a set of contrasts.

Description

This function automates both running romer on a set of contrasts as well as the creation of output HTML tables that can be used to explore the results. The basic idea here is that one might have used limma to fit a model and compute some contrasts, and then want to do a GSEA using romer.

Usage

runRomer(setloc, annot = NULL, eset, design = NULL, contrast = NULL, fit,
  wts = NULL, save = TRUE, baseline.hmap = TRUE, affy = TRUE, ...)

Arguments

setloc

A character vector giving the path for gene set RData files (see description for more information).

annot

Character. The name of the array annotation package.

eset

An ExpressionSet containing normalized expression data.

design

A design matrix describing the model fit to the data.

contrast

A contrast matrix describing the contrasts that were computed from the data. This contrast should have colnames, which will be used to create parts of the resulting directory structure.

fit

An MArrayLM object, containing the fitted model data.

wts

Optional weights vector - if array weights were used to fit the model, they should be supplied here as well.

save

Boolean. If true, after running the romer step, the results will be saved in a file 'romer.Rdata', which can be used as input for outputRomer to create HTML tables. Since romer can take a long time to run, it is advantageous to keep the default.

baseline.hmap

Boolean. If TRUE, then the resulting heatmaps will be centered by subtracting the mean of the baseline sample. As an example, in a contrast of treatment A - treatment B, the mean of the treatment B samples will be subtracted. The heatmap colors then represent the fold change between the A and B samples.

affy

Boolean; are these Affymetrix arrays? If TRUE, the output tables will contain links to the netaffx site.

...

Used to pass arguments to lower-level functions. See outputRomer geneSetPage, dataAndHeatmapPage and gsHeatmap for available arguments.

Value

• Nothing is returned. This function is called only for the side-effects of creating output HTML files in the working and sub-directories.

Details

The romer expects as input a list or lists of gene symbols that represent individual gene sets. One example is the various gene sets from the Broad Institute that are available at http://bioinf.wehi.edu.au/software/MSigDB/, which are distributed as RData files. The default assumption for this function is that the end user will have downloaded these files, and the setloc argument simply tells runRomer where to find them.

Alternatively, user-based gene sets could be created (these should consist of lists of character vectors of gene symbols - see one of the Broad gene sets for an example).

This function will run romer using all the gene sets in the referenced directory, on all the contrasts supplied, and then output the results in a (default) 'genesets' subdirectory. There will be an HTML file in the working directory with a (default) filename of 'indexRomer.html' that will point to individual HTML files in the genesets subdirectory, which will point to individual files in subdirectories within the genesets subdirectory (named after the colnames of the contrast matrix).