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.