R: Map between Manufacturer Identifiers and Gene Symbols
illuminaMousev1p1SYMBOL
R Documentation
Map between Manufacturer Identifiers and Gene Symbols
Description
illuminaMousev1p1SYMBOL is an R object that provides mappings between
manufacturer identifiers and gene abbreviations.
Details
Each manufacturer identifier is mapped to an abbreviation for the
corresponding gene. An NA is reported if there is no known
abbreviation for a given gene.
Symbols typically consist of 3 letters that define either a single
gene (ABC) or multiple genes (ABC1, ABC2, ABC3). Gene symbols can be
used as key words to query public databases such as Entrez Gene.
Mappings were based on data provided by: Entrez Gene
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
With a date stamp from the source of: 2015-Mar17
x <- illuminaMousev1p1SYMBOL
# Get the probe identifiers that are mapped to a gene symbol
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the SYMBOL 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(illuminaMousev1p1.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/illuminaMousev1p1.db/illuminaMousev1p1SYMBOL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1p1SYMBOL
> ### Title: Map between Manufacturer Identifiers and Gene Symbols
> ### Aliases: illuminaMousev1p1SYMBOL
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaMousev1p1SYMBOL
> # Get the probe identifiers that are mapped to a gene symbol
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the SYMBOL for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "Best1"
>
>
>
>
>
> dev.off()
null device
1
>