lumi (version 2.24.0)

nuID2EntrezID: Map nuID to Entrez ID

Description

Map nuID to EntrezID through RefSeq ID based on IDMapping libraries.

Usage

nuID2EntrezID(nuID = NULL, lib.mapping, filterTh = c(Strength1 = 95, Uniqueness = 95), returnAllInfo = FALSE)

Arguments

nuID

a vector of nuIDs. If it is NULL, all mappings will be returned.

lib.mapping

the ID mapping library

filterTh

the mapping quality filtering threshold used to filter the ID mapping.

returnAllInfo

determine to return the detailed mapping information or just the matched RefSeq IDs

Value

returns the matched Entrez IDs or a data.frame with each row corresponding to an input nuID (when "returnAllInfo" is TRUE).

Details

This function is based on the return of getNuIDMappingInfo function. The mapping from nuID to EntrezID was based on the mapping from nuID to RefSeqID and RefSeqID to EntrezID. It uses mapping quality information to filter out the bad mappings from nuID to RefSeqID. The parameter "filterTh" is obsolete for lumi ID mapping package > version 1.3, which only keeps the perfect mapping. For the old version of ID mapping package (< 1.3), the names of "filterTh" are basically the field names of "nuID\_MappingInfo" table, which include 'Strength1', 'Strength2', 'Uniqueness' and 'Total hits'. For the definition of these metrics, please refer to the IDMapping library or see the reference website.

References

https://prod.bioinformatics.northwestern.edu/nuID/

See Also

See Also getNuIDMappingInfo

Examples

	## load example data
	data(example.lumi)
	if (require(lumiHumanIDMapping)) {
		nuIDs <- featureNames(example.lumi)
		mappingInfo <- nuID2EntrezID(nuIDs, lib.mapping='lumiHumanIDMapping')
		head(mappingInfo)
	}