affycoretools (version 1.38.0)

probes2tableBM: Convert Affy Probe ids to Annotated HTML Table using biomaRt

Description

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.

Usage

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)

Arguments

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?

Value

This function is only used for the side effect of outputting an HTML table.

Details

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 listFilters.

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]].

See Also

topTable