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 illuminaMousev1 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
illuminaMousev1listNewMappings()
x <- illuminaMousev1PROBEQUALITY
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 <- illuminaMousev1ARRAYADDRESS
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(illuminaMousev1ARRAYADDRESS)
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 <- illuminaMousev1CODINGZONE
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 <- illuminaMousev1PROBESEQUENCE
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(illuminaMousev1.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.Mm.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaMousev1.db/illuminaMousev1NewMappings.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1listNewMappings
> ### Title: Custom mappings added to the package
> ### Aliases: illuminaMousev1ARRAYADDRESS illuminaMousev1NUID
> ### illuminaMousev1PROBESEQUENCE illuminaMousev1PROBEQUALITY
> ### illuminaMousev1CODINGZONE illuminaMousev1GENOMICLOCATION
> ### illuminaMousev1GENOMICMATCHSIMILARITY illuminaMousev1SECONDMATCHES
> ### illuminaMousev1SECONDMATCHSIMILARITY
> ### illuminaMousev1TRANSCRIPTOMICMATCHSIMILARITY
> ### illuminaMousev1OTHERGENOMICMATCHES illuminaMousev1REPEATMASK
> ### illuminaMousev1OVERLAPPINGSNP illuminaMousev1ENTREZREANNOTATED
> ### illuminaMousev1ENSEMBLREANNOTATED illuminaMousev1SYMBOLREANNOTATED
> ### illuminaMousev1listNewMappings illuminaMousev1fullReannotation
> ### illuminaMousev1REPORTERGROUPNAME illuminaMousev1REPORTERGROUPID
> ### Keywords: datasets
>
> ### ** Examples
>
>
> ##See what new mappings are available
>
> illuminaMousev1listNewMappings()
illuminaMousev1ARRAYADDRESS()
illuminaMousev1PROBESEQUENCE()
illuminaMousev1REPORTERGROUPNAME()
illuminaMousev1REPORTERGROUPID()
illuminaMousev1NUID()
illuminaMousev1PROBEQUALITY()
illuminaMousev1CODINGZONE()
illuminaMousev1SECONDMATCHES()
illuminaMousev1OTHERGENOMICMATCHES()
illuminaMousev1REPEATMASK()
illuminaMousev1OVERLAPPINGSNP()
illuminaMousev1ENTREZREANNOTATED()
illuminaMousev1GENOMICLOCATION()
illuminaMousev1SYMBOLREANNOTATED()
illuminaMousev1ENSEMBLREANNOTATED()
>
>
> x <- illuminaMousev1PROBEQUALITY
>
> 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] "No match"
>
>
> ##Overall table of qualities
> table(unlist(xx))
Bad Good Good*** Good**** No match Perfect
6606 774 146 246 887 30388
Perfect*** Perfect****
6137 810
>
>
>
> x <- illuminaMousev1ARRAYADDRESS
>
> 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] "102450270"
>
> ##Can do the mapping from array address to illumina ID using a revmap
>
> y<- revmap(illuminaMousev1ARRAYADDRESS)
>
> 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] "10181072_239_rc-S"
>
>
>
> x <- illuminaMousev1CODINGZONE
>
> 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 <- illuminaMousev1PROBESEQUENCE
>
> 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] "CAATGAATTCCTTTGCGCCGTTCCTCATGTTTGAAGCACTAACAAAGCAC"
>
>
>
>
>
>
>
> dev.off()
null device
1
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