R: Map between Manufacturer Identifiers and RefSeq Identifiers
lumiHumanAllREFSEQ
R Documentation
Map between Manufacturer Identifiers and RefSeq Identifiers
Description
lumiHumanAllREFSEQ is an R object that provides mappings between
manufacturer identifiers and RefSeq identifiers.
Details
Each manufacturer identifier is mapped to a named vector of RefSeq identifiers. The
name represents the manufacturer identifier and the vector contains all RefSeq
identifiers that can be mapped to that manufacturer identifier. The length of the
vector may be one or greater, depending on how many RefSeq identifiers a given
manufacturer identifier can be mapped to. An NA is reported for any
manufacturer identifier that cannot be mapped to a RefSeq identifier at this time.
RefSeq identifiers differ in format according to the type of record the identifiers
are for as shown below:
NG_XXXXX: RefSeq accessions for genomic region (nucleotide) records
NM_XXXXX: RefSeq accessions for mRNA records
NC_XXXXX: RefSeq accessions for chromosome records
NP_XXXXX: RefSeq accessions for protein records
XR_XXXXX: RefSeq accessions for model RNAs that are not associated with
protein products
XM_XXXXX: RefSeq accessions for model mRNA records
XP_XXXXX: RefSeq accessions for model protein records
x <- lumiHumanAllREFSEQ
# Get the probe identifiers that are mapped to any RefSeq ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the REFSEQ for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(lumiHumanAll.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
lumiHumanAll.db is using or is likely to need access to special nuID
identifiers. Users can learn about these identifiers from vignette
documentation provided with the lumi package.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiHumanAll.db/lumiHumanAllREFSEQ.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanAllREFSEQ
> ### Title: Map between Manufacturer Identifiers and RefSeq Identifiers
> ### Aliases: lumiHumanAllREFSEQ
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- lumiHumanAllREFSEQ
> # Get the probe identifiers that are mapped to any RefSeq ID
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the REFSEQ for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "NM_001014446" "NM_001286773" "NM_001286774" "NM_152398" "NP_001014446"
[6] "NP_001273702" "NP_001273703" "NP_689611" "NR_104589"
>
>
>
>
>
> dev.off()
null device
1
>