Mapping nuIDs of Illumina Human chips to the most recent Homo sapiens RefSeq release

Description

We mapped nuIDs of Illumina Human chips by BLASTing each probe sequence (converted from nuID) against the the most recent Homo sapiens RefSeq release. The mapping also includes the mapping quality information.

Usage

  lumiHumanIDMapping_nuID()

Details

The nuID mapping information is kept in the nuID_MappingInfo table in the ID Mapping library. The nuID mapping table includes following fields (columns):

1. nuID: nuID for the probe sequence

2. Refseq: The refseq IDs with perfect matching with probe sequence. If there are more than one refseq IDs, they are separated by ",".

3. EntrezID: The Entrez gene IDs correspond to the refseq IDs. If there are more than one Entrez gene IDs, they are separated by ",".

4. QualityScore: The mapping quality from probe sequence to RefSeq, see reference 2 for more details.

5. Refseq_old: the refseq ID provided by Illumina company when they designed the chip (included in the chip manifest file).

For the version after 1.4.0, the mapping information was got from the Computational Biology Group at University of Cambridge, see reference link for more details.

Value

lumiHumanIDMapping_nuID returns a nuID mapping summary of Illumina Human chips.

References

1. Du, P., Kibbe, W.A. and Lin, S.M., "nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays", Biology Direct 2007, 2:16 (31May2007). 2. http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html

Examples

  ## List the fields in the nuID_MappingInfo table
  library(DBI)
  conn <- lumiHumanIDMapping_dbconn()
  dbListFields(conn, 'nuID_MappingInfo')

  ## Summary of nuID mapping
  lumiHumanIDMapping_nuID()

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(lumiHumanIDMapping)
Loading required package: lumi
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiHumanIDMapping/lumiHumanIDMapping_nuID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanIDMapping_nuID
> ### Title: Mapping nuIDs of Illumina Human chips to the most recent Homo
> ###   sapiens RefSeq release
> ### Aliases: lumiHumanIDMapping_nuID
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   ## List the fields in the nuID_MappingInfo table
>   library(DBI)
>   conn <- lumiHumanIDMapping_dbconn()
>   dbListFields(conn, 'nuID_MappingInfo')
[1] "nuID"      "Accession" "EntrezID"  "Symbol"   
> 
>   ## Summary of nuID mapping
>   lumiHumanIDMapping_nuID()
nuID_MappingInfo table includes 105521 unique Homo sapiens Illumina probes mapping information.

The table includes following fields (see help(lumiHumanIDMapping_nuID) for detailed definition.):
nuID
	Accession
	EntrezID
	Symbol
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>