nuID2IlluminaID {lumi} | R Documentation |
Matching nuIDs to Illumina IDs based on Illumina ID mapping library
nuID2IlluminaID(nuID, lib.mapping=NULL, species = c("Human", "Mouse", "Rat", "Unknown"), idType=c('All', 'Probe', 'Gene', 'Accession', 'Search_key', 'Symbol'), chipVersion = NULL, ...)
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 |
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.
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.
Pan Du
## load example data data(example.lumi) nuIDs <- featureNames(example.lumi) if (require(lumiHumanIDMapping)) { illuminaID <- nuID2IlluminaID(nuIDs[1:5], lib='lumiHumanIDMapping') illuminaID }