nuID2IlluminaID: Matching nuIDs to Illumina IDs based on Illumina ID mapping...

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

Description

Matching nuIDs to Illumina IDs based on Illumina ID mapping library

Usage

nuID2IlluminaID(nuID, lib.mapping=NULL, species = c("Human", "Mouse", "Rat", "Unknown"), idType=c('All', 'Probe', 'Gene', 'Accession', 'Search_key', 'Symbol'), chipVersion = NULL, ...)

Arguments

nuID	a vector of nuIDs
lib.mapping	the ID mapping library. If it is provided, the parameter "species" will be ignored.
species	the species of the chip designed for. If users do not know it, it can be set as "Unknown".
idType	the Illumina ID type
chipVersion	chipVersion information returned by function getChipInfo
...	other parameters of getChipInfo

Details

The parameter "idType" represents different types of Illumina IDs. It returns the entire table when idType = "All". When idType = 'Probe', it returns "ProbeId" or "Probe\_Id". When idType = 'Gene', it returns "Target" or "ILMN\_Gene" IDs.

This function basically returned the "idMapping" item returned by function getChipInfo. If nuID is NULL and chipVersion is provided, it will return all mapping information of the chip.

Value

The mapping information from nuID to Illumina ID. It will be a matrix with each column corresponding to one matched manifest file when parameter "returnAllMatches" is TRUE. In this case, the columns are sorted from the best match to worst.

Author(s)

Pan Du

See Also

getChipInfo, IlluminaID2nuID

Examples

	## load example data
	data(example.lumi)
	nuIDs <- featureNames(example.lumi)
	if (require(lumiHumanIDMapping)) {
		illuminaID <- nuID2IlluminaID(nuIDs[1:5], lib='lumiHumanIDMapping')
		illuminaID
	}

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