findLargest: Find the Entrez Gene ID corresponding to the largest...

In genefilter: genefilter: methods for filtering genes from high-throughput experiments

Description

Most microarrays have multiple probes per gene (Entrez). This function finds all replicates, and then selects the one with the largest value of the test statistic.

Usage

findLargest(gN, testStat, data = "hgu133plus2")

Arguments

gN	A vector of probe identifiers for the chip.
testStat	A vector of test statistics, of the same length as gN with the per probe test statistics.
data	The character string identifying the chip.

Details

All the probe identifiers, gN, are mapped to Entrez Gene IDs and the duplicates determined. For any set of probes that map to the same Gene ID, the one with the largest test statistic is found. The return vector is the named vector of selected probe identifiers. The names are the Entrez Gene IDs.

This could be extended in different ways, such as allowing the user to use a different selection criterion. Also, matching on different identifiers seems like another alternative.

Value

A named vector of probe IDs. The names are Entrez Gene IDs.

Author(s)

R. Gentleman

See Also

sapply

Examples

  library("hgu95av2.db")
  set.seed(124)
  gN <- sample(ls(hgu95av2ENTREZID), 200)
  stats <- rnorm(200)
  findLargest(gN, stats, "hgu95av2")

genefilter documentation built on Jan. 23, 2021, 2:01 a.m.