PMIDAmat: A function to compute the probe to PubMed id incidence...

In Bioconductor/annotate: Annotation for microarrays

A function to compute the probe to PubMed id incidence matrix.

Description

For a given chip or a given set of genes, it computes the mapping from probes to PubMed id.

Usage

PMIDAmat(pkg, gene=NULL)

Arguments

pkg	The package name of the chip for which the incidence matrix should be computed.
gene	A character vector of interested probe set ids or NULL (default).

Details

Not much to say, just find which probes are associated with which PubMed ids and return the incidence matrix, with PubMed ids as rows and probes as columns.

To specify a set of probes to use, let the argument gene to be a vector of probe ids. Bt this way, the calculations are not involved with non-interested genes/PubMed ids so that the whole process could finish soon.

Value

A matrix containing zero or one, depending on whether the probe (column) is associated with a PubMed id (row).

Author(s)

R. Gentleman

Examples

  library("hgu95av2.db")
  probe <- names(as.list(hgu95av2ACCNUM))
  Amat <- PMIDAmat("hgu95av2", gene=sample(probe, 10))

Bioconductor/annotate documentation built on Nov. 2, 2024, 4:40 p.m.