limma2annaffy {affycoretools} | R Documentation |
This function is designed to take an ExpressionSet
and an lmFit
, model.matrix
,
and contrast object from limma and convert into HTML tables using
annaffy. The alternate function limma2annaffy.na
is designed to
be run without user intervention.
limma2annaffy(eset, fit, design, contrast, lib, adjust = "fdr", anncols = aaf.handler()[c(1:3, 7:8, 10:13)], number = 30, pfilt = NULL, fldfilt= NULL,tstat = TRUE, pval = TRUE, FC = TRUE, expression = TRUE, html = TRUE, text = FALSE, save = FALSE, addname = NULL, interactive = TRUE)
eset |
An ExpressionSet containing affymetrix
expression values. |
fit |
An lmFit object. |
design |
A model.matrix object. |
contrast |
A contrasts matrix from limma. |
lib |
An annotation package for the Affy chips used. |
adjust |
Multiplicity adjustment. Choices are "fdr","holm","hommel","bonferroni", or "none". Partial matching allowed. |
anncols |
A vector of things to annotate, produced by a call to aaf.handler(). |
number |
Number of genes to output to table. See details for more information. |
pfilt |
A p-value to filter output. See details for more information. |
fldfilt |
A fold change to filter output. See details for more information. |
tstat |
Boolean: Output t-statistics in table? Defaults to FALSE . |
pval |
Boolean: Output (adjusted) p-values in table?
Defaults to FALSE . |
FC |
Boolean: Output fold changes in table? Defaults to FALSE . |
expression |
Boolean: Output expression values in
table? Defaults to TRUE . |
html |
Boolean: Output data in HTML tables? Defaults to TRUE . |
text |
Boolean: Output data in text tables? Defaults to TRUE . |
save |
Boolean: Save tables as R objects for further
processing? Defaults to FALSE . |
addname |
A character vector to add to the end of the automatically generated output file names. Useful for multiple calls to eliminate over-writing of existing HTML or text tables. |
interactive |
Boolean: Is this an interactive call, or run as
part of a script (e.g., in an Sweave document)? Defaults to TRUE |
This function is designed to automatically output HTML or text tables,
with filenames taken from the column names of the contrast matrix. The
number of genes output can be controlled several different
ways. First, if pfilt and fldfilt are both NULL
, the top genes
will be output based on the number
variable. Otherwise, the
genes are filtered based on p-value, fold change, or both. If the
genes are filtered this way, the number of genes to be output will be
listed and the filter(s) can then be adjusted if necessary.
This function currently only supports Affymetrix data.
If save
is TRUE
, a list of tables from
topTable
will be output.
James W. MacDonald <jmacdon@med.umich.edu>