jscores {jetset}

Retrieve jetset scores for probe sets

Description

This function retrieves jetset scores, which indicate the predicted quality of individual probe sets on selected Affymetrix microarrays.

Usage

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

Arguments

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)

Details

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.

Value

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.

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

Examples

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

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