R: Mappings between probe identifiers and KEGG pathway...
illuminaRatv1PATH
R Documentation
Mappings between probe identifiers and KEGG pathway identifiers
Description
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
for various organisms.
illuminaRatv1PATH maps probe identifiers to the identifiers used by
KEGG for pathways in which the genes represented by the probe
identifiers are involved
illuminaRatv1PATH2PROBE is an R object that provides mappings between
KEGG identifiers and manufacturer identifiers.
Details
Each KEGG pathway has a name and identifier. Pathway name for a given pathway
identifier can be obtained using the KEGG data package that can either be
built using AnnBuilder or downloaded from Bioconductor
http://www.bioconductor.org.
Graphic presentations of pathways are searchable at
url http://www.genome.ad.jp/kegg/pathway.html by using pathway identifiers as
keys.
Mappings were based on data provided by: KEGG GENOME
ftp://ftp.genome.jp/pub/kegg/genomes
With a date stamp from the source of: 2011-Mar15
x <- illuminaRatv1PATH
# Get the probe identifiers that are mapped to a KEGG pathway ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the PATH for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
# Now convert the illuminaRatv1PATH2PROBE object to a list
xx <- as.list(illuminaRatv1PATH2PROBE)
if(length(xx) > 0){
# Get the probe identifiers for the first two pathway identifiers
xx[1:2]
# Get the first one
xx[[1]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaRatv1.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.Rn.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaRatv1.db/illuminaRatv1PATH.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaRatv1PATH
> ### Title: Mappings between probe identifiers and KEGG pathway identifiers
> ### Aliases: illuminaRatv1PATH illuminaRatv1PATH2PROBE
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaRatv1PATH
> # Get the probe identifiers that are mapped to a KEGG pathway ID
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the PATH for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "00040" "00053" "00140" "00500" "00514" "00830" "00860" "00980" "00982"
[10] "00983" "01100" "04976"
>
> # Now convert the illuminaRatv1PATH2PROBE object to a list
> xx <- as.list(illuminaRatv1PATH2PROBE)
> if(length(xx) > 0){
+ # Get the probe identifiers for the first two pathway identifiers
+ xx[1:2]
+ # Get the first one
+ xx[[1]]
+ }
[1] "ILMN_1358051" "ILMN_1367246" "ILMN_1363231" "ILMN_1373027" "ILMN_1371606"
[6] "ILMN_1372407" "ILMN_1359563" "ILMN_1369837" "ILMN_1358775" "ILMN_1349133"
[11] "ILMN_1359634" "ILMN_1375640" "ILMN_1351123" "ILMN_1358507" "ILMN_1362372"
[16] "ILMN_1359245" "ILMN_1349219" "ILMN_1364579" "ILMN_1351156" "ILMN_1350196"
[21] "ILMN_1370405" "ILMN_1650785" "ILMN_1360909" "ILMN_1360951" "ILMN_1366612"
[26] "ILMN_1358403" "ILMN_1367148" "ILMN_1350645" "ILMN_1362844" "ILMN_1366908"
[31] "ILMN_1350459" "ILMN_1370411" "ILMN_1364888" "ILMN_1366363" "ILMN_1352501"
[36] "ILMN_1356340" "ILMN_1371561" "ILMN_1376791" "ILMN_1649829" "ILMN_1367964"
[41] "ILMN_1355584" "ILMN_1365964" "ILMN_1349648" "ILMN_1352752" "ILMN_1373467"
[46] "ILMN_1356435" "ILMN_1369041" "ILMN_1365179" "ILMN_1364458" "ILMN_1349290"
[51] "ILMN_1358673" "ILMN_1369385" "ILMN_1361975" "ILMN_2039699" "ILMN_1364240"
[56] "ILMN_1368450" "ILMN_1371877" "ILMN_1530434" "ILMN_1351669" "ILMN_1372453"
[61] "ILMN_1356105" "ILMN_1370258" "ILMN_1361218" "ILMN_1376649" "ILMN_1363479"
[66] "ILMN_1376969" "ILMN_1376325" "ILMN_1357187" "ILMN_1358623" "ILMN_1373258"
[71] "ILMN_1362768" "ILMN_1357483" "ILMN_1376830" "ILMN_1359521" "ILMN_1370772"
[76] "ILMN_1370756" "ILMN_1649854" "ILMN_1348896"
>
>
>
>
>
> dev.off()
null device
1
>