addNuID2lumi: Add the nuID information to the LumiBatch object

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

Description

Replace the Illumina Id (Target ID or Probe Id) as nuID (nucleotide universal identifier) for indexing genes in the LumiBatch object

Usage

addNuID2lumi(x.lumi, annotationFile=NULL, sep = NULL, lib.mapping = NULL,  annotationColName = c(sequence = "Probe_Sequence", target = "ILMN_Gene", probe='Probe_Id'), verbose = TRUE)

Arguments

x.lumi	a LumiBatch object
annotationFile	a annotation file, which includes the Illumina ID (target or probe ids) and probe sequence information
sep	the separation used in the annotation file. Automatically detect the separator if it is "," or "\t".
lib.mapping	a Illumina ID mapping package, e.g, lumiHumanIDMapping
annotationColName	the annotation column name in the annotation file used for the probe sequence and TargetID and ProbeID
verbose	a boolean to decide whether to print out some messages

Details

Since the default Illumina IDs (TargetID (ILMN\_Gene ID) and ProbeId (Probe\_Id)) are not consistent between different arrays and batches, we invented a nuID, which is one-to-one matching with the probe sequence. This function is to replace the Illumina ID with the nuID. If the annotation library (the unzipped manifest file (.bgx)) is provided, the function will automatically check whether the Illumina ID is provided for the microarray data. We recommend output the data using ProbeID when using Illumina BeadStudio software, because the TargetID (ILMN\_Gene ID) are not unique.

Value

a LumiBatch object with Illumina ID replaced by nuID.

Author(s)

Pan Du

References

Du, P., Kibbe, W.A., Lin, S.M., "nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays", submitted.

See Also

IlluminaID2nuID, lumiR

Examples

## load example data
# data(example.lumi)

## specify the annotation file for the Illumina chip
# annotationFile <- 'Human_RefSeq-8.csv'
## Replace the Target ID with nuID
# lumi.nuID <- addNuID2lumi(example.lumi, annotationFile)

## An alternative way is to load the Annotation library and match the targetID (or Probe Id) with nuID
# lumi.nuId <- addNuID2lumi(example.lumi, lib.mapping='lumiHumanIDMapping')

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