dataAndHeatmapPage: A function to create an annotated HTML table for all genes in...

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

A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data.

Description

This is intended to be an internal function to runRomer. It is documented here only because it may be necessary to pass alternative arguments to this function from runRomer.

Usage

dataAndHeatmapPage(
  object,
  fit,
  ind,
  columns = NULL,
  fname,
  heatmap,
  title,
  key = TRUE,
  fitind = NULL,
  affy = TRUE,
  ...
)

Arguments

object	An ExpressionSet, containing normalized, summarized gene expression data.
fit	An MArrayLM object containing the fitted data.
ind	Numeric vector indicating which rows of the data object to use.
columns	Numeric vector indicating which columns of the data object to use. If NULL, all columns will be used.
fname	The filename of the resulting output, without the 'html' file extension.
heatmap	Character. The filename of the heatmap to append to the bottom of the HTML page.
title	Title to be placed at the top of the resulting HTML page.
key	Character. The filename of the heatmap key to append to the bottom of the HTML page.
fitind	Numeric. Which column of the MArrayLM object to use for output in the HTML table.
affy	Boolean. Are these Affymetrix arrays? If TRUE, then links will be generated to netaffx for the probeset IDs.
...	Included to allow arbitrary commands to be passed to lower level functions.

Details

This function creates an annotation table using probes2table if an annotation file is used, otherwise data will be output in a simple HTML table. A heatmap showing the expression values for all the genes in the gene set is then placed below this table, along with a key that indicates the range of the expression values.

Author(s)

James W. MacDonald <[e-mail]>

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.