affy (version 1.50.0)

geneSetPage: A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set.

Description

This is intended to be an internal function to runRomer, and is not intended to be called by end users. However, the ...

Usage

geneSetPage(rslts, genesets, eset, fit, file, cutoff = 0.05, dir = ".",
  subdir = ".", columns = NULL, colnames = NULL, col = NULL,
  caption = NULL, fitind = NULL, bline = NULL, affy = TRUE, ...)

Arguments

rslts
The results from running romer on one gene set.
genesets
Character. A vector of gene symbols for one gene set.
eset
An ExpressionSet containing normalized, summarized gene expression data.
fit
An MArrayLM object, containing the fitted data.
file
Filename for the resulting HTML page.
cutoff
Numeric. The cutoff for significance for a given gene set. Defaults to 0.05.
dir
The directory to write the results. Defaults to the working directory.
subdir
The subdirectory to write the individual gene set results. Defaults to the working directory.
columns
Numeric. The columns of the ExpressionSet to use for the individual gene set output pages. See dataAndHeatmapPage for more information.
colnames
Character. Alternative column names for the resulting heatmap. See dataAndHeatmapPage for more information.
col
A vector of colors for the heatmap. Defaults to bluered.
caption
Caption to put at the top of the HTML page.
fitind
Numeric. The columns of the MArrayLM object to use for the individual HTML tables.
bline
Defaults to NULL. Otherwise, a numeric vector indicating which columns of the data are the baseline samples. The data used for the heatmap will be centered by subtracting the mean of these columns from all data.
affy
Boolean; are these Affymetrix arrays? If TRUE, the Affymetrix probeset IDs will contain links to the netaffx site.
...
Allows arguments to be passed to lower-level functions. See dataAndHeatmapPage and gsHeatmap for available arguments.

Value

  • Nothing is returned. Called only for the side effect of creating HTML tables.

code

runRomer

Details

This function creates a midlevel HTML table that contains each gene set that was significant, with a link to an HTML table that shows data for each gene in that gene set (with annotation), as well as a heatmap showing the expression levels. Normally this is not run by end users, but is called as part of the runRomer function.