jscores: Retrieve jetset scores for 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 jetset scores, which indicate the predicted quality of individual probe sets on selected Affymetrix microarrays.

1	jscores(chip, probeset, eg, symbol, alias, ensembl)

`chip`	Chip name
`probeset`	A vector of probe set IDs (optional)
`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". If no further arguments are specified, the scores for all probe sets on the chip are returned.

If any of probeset, eg, symbol, alias, or ensembl are specified, these are used to filter the resulting data frame in a logical OR sense.

Details about the jetset algorithm are available in the vignette.

A data frame in which each row corresponds to a probe set, with 8 columns:

`EntrezID`	Entrez GeneID of the targeted gene (character).
`nProbes`	Number of probes in the probe set (integer).
`process`	Processivity requirement (integer).
`specificity`	Specificity score (numeric).
`coverage`	Coverage score (numeric).
`robust`	Robustness score (numeric).
`overall`	Overall score (numeric).
`symbol`	HUGO gene symbol (character).

The rows are sorted by decreasing overall score.

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 data comes from (e.g.) scores.hgu95av2, with gene symbol lookups coming from org.Hs.egSYMBOL.

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

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