Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Custom mappings added to the packageDescriptionWe have used an extensive re-annotation of the illuminaHumanv2 probe sequences to provide additional information that is not captured in the standard Bioconductor packages. Whereas Bioconductor annotations are based on the RefSeq ID that each probe maps to, our additional mappings provide data specific to each probe on the platform. See below for details. We recommend using the probe quality as a form of filtering, and retaining only perfect or good probes for an analysis. Details of custom mappings
Referenceshttp://remoat.sysbiol.cam.ac.uk Barbosa-Morais et al. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research Examples
##See what new mappings are available
illuminaHumanv2listNewMappings()
x <- illuminaHumanv2PROBEQUALITY
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the PROBEQUALITY for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
##Overall table of qualities
table(unlist(xx))
x <- illuminaHumanv2ARRAYADDRESS
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the ARRAYADDRESS for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
##Can do the mapping from array address to illumina ID using a revmap
y<- revmap(illuminaHumanv2ARRAYADDRESS)
mapped_probes <- mappedkeys(y)
# Convert to a list
yy <- as.list(y[mapped_probes])
if(length(yy) > 0) {
# Get the ARRAYADDRESS for the first five probes
yy[1:5]
# Get the first one
yy[[1]]
}
x <- illuminaHumanv2CODINGZONE
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the CODINGZONE for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
x <- illuminaHumanv2PROBESEQUENCE
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the PROBESEQUENCE for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
Results
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> library(illuminaHumanv2.db)
Loading required package: AnnotationDbi
Loading required package: stats4
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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
Loading required package: org.Hs.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaHumanv2.db/illuminaHumanv2NewMappings.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2listNewMappings
> ### Title: Custom mappings added to the package
> ### Aliases: illuminaHumanv2ARRAYADDRESS illuminaHumanv2NUID
> ### illuminaHumanv2PROBESEQUENCE illuminaHumanv2PROBEQUALITY
> ### illuminaHumanv2CODINGZONE illuminaHumanv2GENOMICLOCATION
> ### illuminaHumanv2GENOMICMATCHSIMILARITY illuminaHumanv2SECONDMATCHES
> ### illuminaHumanv2SECONDMATCHSIMILARITY
> ### illuminaHumanv2TRANSCRIPTOMICMATCHSIMILARITY
> ### illuminaHumanv2OTHERGENOMICMATCHES illuminaHumanv2REPEATMASK
> ### illuminaHumanv2OVERLAPPINGSNP illuminaHumanv2ENTREZREANNOTATED
> ### illuminaHumanv2ENSEMBLREANNOTATED illuminaHumanv2SYMBOLREANNOTATED
> ### illuminaHumanv2listNewMappings illuminaHumanv2fullReannotation
> ### illuminaHumanv2REPORTERGROUPNAME illuminaHumanv2REPORTERGROUPID
> ### Keywords: datasets
>
> ### ** Examples
>
>
> ##See what new mappings are available
>
> illuminaHumanv2listNewMappings()
illuminaHumanv2ARRAYADDRESS()
illuminaHumanv2NUID()
illuminaHumanv2PROBEQUALITY()
illuminaHumanv2CODINGZONE()
illuminaHumanv2PROBESEQUENCE()
illuminaHumanv2SECONDMATCHES()
illuminaHumanv2OTHERGENOMICMATCHES()
illuminaHumanv2REPEATMASK()
illuminaHumanv2OVERLAPPINGSNP()
illuminaHumanv2ENTREZREANNOTATED()
illuminaHumanv2GENOMICLOCATION()
illuminaHumanv2SYMBOLREANNOTATED()
illuminaHumanv2REPORTERGROUPNAME()
illuminaHumanv2REPORTERGROUPID()
illuminaHumanv2ENSEMBLREANNOTATED()
>
>
> x <- illuminaHumanv2PROBEQUALITY
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the PROBEQUALITY for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "Perfect***"
>
>
> ##Overall table of qualities
> table(unlist(xx))
Bad Good Good*** Good**** No match Perfect
15528 792 180 317 2674 20671
Perfect*** Perfect****
7709 1610
>
>
>
> x <- illuminaHumanv2ARRAYADDRESS
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the ARRAYADDRESS for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "2100682"
>
> ##Can do the mapping from array address to illumina ID using a revmap
>
> y<- revmap(illuminaHumanv2ARRAYADDRESS)
>
> mapped_probes <- mappedkeys(y)
> # Convert to a list
> yy <- as.list(y[mapped_probes])
> if(length(yy) > 0) {
+ # Get the ARRAYADDRESS for the first five probes
+ yy[1:5]
+ # Get the first one
+ yy[[1]]
+ }
[1] "ILMN_1910180"
>
>
>
> x <- illuminaHumanv2CODINGZONE
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the CODINGZONE for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "Transcriptomic?"
>
> x <- illuminaHumanv2PROBESEQUENCE
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the PROBESEQUENCE for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "ACACCTTCAGGAGGGAAGCCCTTATTTCTGGGTTGAACTCCCCTTCCATG"
>
>
>
>
>
>
>
> dev.off()
null device
1
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