jmap: Retrieve jetset mapped probe sets
In jetset: One-to-One Gene-Probeset Mapping for Affymetrix Human Microarrays

Description Usage Arguments Details Value References See Also Examples

This function retrieves probe sets corresponding to the queried genes

1	jmap(chip, eg, symbol, alias, ensembl)

`chip`	Chip name
`eg`	A vector of Entrez GeneIDs (optional)
`symbol`	A vector of gene symbols (optional)
`alias`	A vector of gene aliases (optional)
`ensembl`	A vector of Ensembl IDs (optional)

Currently, chip can be "hgu95av2", "hgu133a", "hgu133plus2", or "u133x3p".

Queried genes must be specified by either eg, symbol, alias, or ensembl.

If the query is not recognized, or is ambiguous, or corresponds to a gene that is not detected by the array, NA will be returned.

Details about the jetset algorithm are available in the vignette.

A character vector of probe set IDs

Qiyuan Li, Nicolai J. Birkbak, Balazs Gyorffy, Zoltan Szallasi and Aron C. Eklund. (2011) Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics. 12:474.

The underlying Entrez ID to probeset data is available in (e.g.) scores.hgu95av2. Symbol, alias, and ensembl lookups are generated from e.g. org.Hs.egSYMBOL2EG.

  genes <- c('MKI67', 'CHD5', 'ESR1', 'FGF19', 'ERBB2', 'NoSuchGene')

  # This generates several informative warnings
  jmap('hgu133a', symbol = genes)