R: Maps between Manufacturer IDs and Enzyme Commission (EC)...
illuminaHumanv3ENZYME
R Documentation
Maps between Manufacturer IDs and Enzyme Commission (EC) Numbers
Description
illuminaHumanv3ENZYME is an R object that provides mappings between
manufacturer identifiers and EC numbers.
illuminaHumanv3ENZYME2PROBE is an R object that maps Enzyme Commission
(EC) numbers to manufacturer identifiers.
Details
When the illuminaHumanv3ENZYME maping viewed as a list, each
manufacturer identifier maps to a named vector containing the EC
number that corresponds to the enzyme produced by that gene. The names
corresponds to the manufacturer identifiers. If this information is
unknown, the vector will contain an NA.
For the illuminaHumanv3ENZYME2PROBE, each EC number maps to a named
vector containing all of the manufacturer identifiers that correspond
to the gene that produces that enzyme. The name of the vector
corresponds to the EC number.
Enzyme Commission numbers are assigned by the Nomenclature Committee
of the International Union of Biochemistry and Molecular Biology
http://www.chem.qmw.ac.uk/iubmb/enzyme/ to allow enzymes to be
identified.
An Enzyme Commission number is of the format EC x.y.z.w, where x, y, z,
and w are numeric numbers. In illuminaHumanv3ENZYME2PROBE, EC is dropped from the
Enzyme Commission numbers.
Enzyme Commission numbers have corresponding names that describe the
functions of enzymes in such a way that EC x is a more general
description than EC x.y that in turn is a more general description than
EC x.y.z. The top level EC numbers and names are listed below:
Mappings between probe identifiers and enzyme identifiers were obtained using files
provided by: KEGG GENOME
ftp://ftp.genome.jp/pub/kegg/genomes
With a date stamp from the source of: 2011-Mar15
x <- illuminaHumanv3ENZYME
# Get the probe identifiers that are mapped to an EC number
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the ENZYME for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
# Now convert illuminaHumanv3ENZYME2PROBE to a list to see inside
xx <- as.list(illuminaHumanv3ENZYME2PROBE)
if(length(xx) > 0){
# Get the probe identifiers for the first five enzyme
#commission numbers
xx[1:5]
# Get the first one
xx[[1]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaHumanv3.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/illuminaHumanv3.db/illuminaHumanv3ENZYME.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv3ENZYME
> ### Title: Maps between Manufacturer IDs and Enzyme Commission (EC) Numbers
> ### Aliases: illuminaHumanv3ENZYME illuminaHumanv3ENZYME2PROBE
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaHumanv3ENZYME
> # Get the probe identifiers that are mapped to an EC number
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the ENZYME for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "2.3.1.5"
>
> # Now convert illuminaHumanv3ENZYME2PROBE to a list to see inside
> xx <- as.list(illuminaHumanv3ENZYME2PROBE)
> if(length(xx) > 0){
+ # Get the probe identifiers for the first five enzyme
+ #commission numbers
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "ILMN_1688071" "ILMN_1708402" "ILMN_1743055" "ILMN_1670903"
>
>
>
>
>
> dev.off()
null device
1
>