nuID2RefSeqID: Map nuID to RefSeq ID

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

Description

Map nuID to RefSeq ID based on IDMapping libraries.

Usage

nuID2RefSeqID(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. Obsolete for lumi ID mapping package > version 1.3!
returnAllInfo	determine to return the detailed mapping information or just the matched RefSeq IDs

Details

This function is based on the return of getNuIDMappingInfo function. It uses mapping quality information to filter out the bad mappings. The parameter "filterTh" is obsolete for lumi ID mapping package 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.

Value

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

Author(s)

Warren Kibbe, Pan Du, Simon Lin

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 <- nuID2RefSeqID(nuIDs, lib.mapping='lumiHumanIDMapping')
		head(mappingInfo)
	}

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