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

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

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 ... argument to runRomer allows one to pass arguments to lower level functions, so the arguments are described here.

Usage

geneSetPage(
  rslts,
  genesets,
  object,
  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.
object	An ExpressionSet, DGEList or EList containing normalized, summarized gene expression data.
fit	An MArrayLM or DGEGLM 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.

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.

Value

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

Author(s)

James W. MacDonald <[e-mail]>

jmacdon/affycoretools documentation built on Feb. 25, 2023, 4:51 a.m.