probes2tableBM {affycoretools} | R Documentation |
A function to convert a vector of Affy ids to an annotated HTML or text
table. This function is very similar to probes2table
, except it
uses the biomaRt
package to annotate genes, and the
annotate
package to create the HTML table.
probes2tableBM(eset, probids, species, filename, otherdata = NULL, links = linksBM()[1:3], otherann = annBM()[1:3], ann.source = "entrezgene", express = TRUE, html = TRUE, text = TRUE, affyid = FALSE, mysql = TRUE)
eset |
An ExpressionSet containing Affy expression
values. |
probids |
A vector of probe ids. |
species |
The species name. This must be in a particular format for biomaRt. An example for human is "hsapiens" or for mouse is "mmusculus". |
filename |
File name of the resulting HTML table. |
otherdata |
A *named* list of additional information to include in the resulting table. Examples would be t-statistics, p-values, fold change, etc. Each list item should be a vector the same length as the probids vector. The name associated with each list item will be used as the column name in the resulting table. |
links |
A character vector of things to annotate with hyperlinks
to online databases. See linksBM for possible values. |
otherann |
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. |
express |
Output expression values in table?
Defaults to TRUE . |
html |
Boolean. Output HTML table? Defaults to TRUE |
text |
Boolean. Output text table? 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 output HTML tables based on a set of IDs. 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]]
.
This function is only used for the side effect of outputting an HTML table.
James W. MacDonald <jmacdon@med.umich.edu>