limma2biomaRt {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 and text tables using
biomaRt. The alternate function limma2biomaRt.na
is designed to
be run without user intervention.
limma2biomaRt(eset, fit, design, contrast, species, links = linksBM()[1:3], otherdata = annBM()[1:3], ann.source = "entrezgene", adjust = "fdr", number = 30, pfilt = NULL, fldfilt = NULL, tstat = TRUE, pval = TRUE, FC = TRUE, expression = TRUE, html = TRUE, text = TRUE, save = FALSE, addname = NULL, interactive = TRUE, affyid = FALSE, mysql = TRUE)
eset |
An ExpressionSet containing affymetrix
expression values. |
fit |
An lmFit object. |
design |
A model.matrix object. |
contrast |
A contrasts matrix from limma. |
species |
The species name. This must be in a particular format for biomaRt. An example for human is "hsapiens", or for mouse "mmusculus". |
links |
A character vector of things to annotate with hyperlinks
to online databases. See linksBM for possible values. |
otherdata |
A character vector of things to annotate with text
only (i.e., no hyperlinks). See annBM for possible values. |
ann.source |
The annotation source of the IDs that will be used to annotate the genes. The default value is "entrezgene". See details for other possibilities. |
adjust |
Multiplicity adjustment. Choices are "fdr","holm","hommel","bonferroni", or "none". Partial matching allowed. |
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 |
affyid |
Boolean. Are the IDs used to annotate these data Affymetrix IDs? |
mysql |
Boolean. Should biomaRt use RMySQL to
connect to the Biomart? Default is TRUE because the
RCurl interface of biomaRt is very slow for more than
a few genes. |
This function is designed to automatically output HTML 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. It is designed for Affymetrix chips that don't have an annotation package, which includes data that have been analyzed using the 're-mapped' CDFs supplied to BioC by MBNI at University of Michigan.
The IDs that will be used to annotate the genes depend on the source
of the data. If, for example, one is using an Affymetrix chip that
doesn't have a BioC annotation package, then the IDs will be
Affymetrix IDs. To find out the correct name to use for the ann.source
argument, one can create a connection to a Biomart database using
useMart
and then get a list of available Affy
arrays using getAffyArrays
.
If one is using one of the re-mapped CDFs from MBNI at University of
Michigan, then the IDs to use depend on the mapping used to create the
CDF. At this time, only three types of CDFs can be used; EntrezGene,
UniGene, and RefSeq. One can determine the correct ann.source argument
by creating a connection to a Biomart database, and then calling
linksBM(mart, linksBM())[[3]]
.
If save
is TRUE
, a list of tables from
topTable
will be output.
James W. MacDonald <jmacdon@med.umich.edu>