jmap {jetset}

Retrieve jetset mapped probe sets

Description

This function retrieves probe sets corresponding to the queried genes

Usage

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

Arguments

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)

Details

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.

Value

A character vector of probe set IDs

References

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.

See Also

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.

Examples

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

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