getChipInfo: Get Illumina Chip Information based on probe identifiers

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

Retrieve the matched Illumina chip information by searching the provided probe identifiers through the Illumina identifiers in all manifest files.

Usage

getChipInfo(x, lib.mapping = NULL, species = c("Human", "Mouse", "Rat", "Unknown"), chipVersion = NULL, idMapping = FALSE, returnAllMatches = FALSE, verbose = TRUE)

Arguments

x	a vector of probe identifiers, ExpressionSet object or a matrix with probe identifiers as row names
lib.mapping	the ID mapping library. If it is provided, the parameter "species" will be ignored.
species	species of the chip designed for. If users do not know it, it can be set as "Unknown".
chipVersion	chipVersion information returned by function getChipInfo
idMapping	determine whether return the idMapping information (between Illumina ID and nuID)
returnAllMatches	determine whether return all matches or just the best match
verbose	determine whether print some warning information

Details

The function searches the provided probe Identifiers (Illumina IDs or nuIDs) through all the manifest file ID information kept in the IDMapping libraries (lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping). The Illumina IDs kept in the library include "Search\_key" ("Search\_Key"), "Target" ("ILMN\_Gene"), "Accession", "Symbol", "ProbeId" ("Probe\_Id"). To determine the best match, the function calculate the number of matched probes. The higher "matchedProbeNumber" is claimed as better. When the "matchedProbeNumber" is the same, the manifest file with fewer probes is claimed as better. If x is NULL and chipVersion is provided, it will return the entire mapping table of the chip.

Value

The function returns a list with following items:

chipVersion	the file name of the manifest file for the corresponding version and release
species	the species of the chip designed for
IDType	the type of probe identifier
chipProbeNumber	the number of probes in the manifest file
matchedProbeNumber	the number of input probes matching the manifest file
idMapping	id mapping information between Illumina ID and nuID

When parameter "returnAllMatches" is TRUE, the items of "chipVersion", "IDType", "chipProbeNumber", "inputProbeNumber", "matchedProbeNumber" will be a vector corresponding to the matched manifest files, whose "matchedProbeNumber" is larger than zero, and the "idMapping" will be a matrix with each column corresponding to one matched manifest file. All of the items are sorted from the best match to worst (The higher "matchedProbeNumber" is claimed as better. When the "matchedProbeNumber" is the same, the manifest file with fewer probes is claimed as better.).

Author(s)

Pan Du

See Also

nuID2IlluminaID, IlluminaID2nuID

Examples

	## load example data
	data(example.lumi)
	if (require(lumiHumanIDMapping)) {
		chipInfo <- getChipInfo(example.lumi, species='Human')
		chipInfo
	}

lumi documentation built on Nov. 8, 2020, 5:27 p.m.