R: Map between Common Gene Symbol Identifiers and Manufacturer...
indacALIAS2PROBE
R Documentation
Map between Common Gene Symbol Identifiers and Manufacturer Identifiers
Description
indacALIAS is an R object that provides mappings between
common gene symbol identifiers and manufacturer identifiers.
Details
Each gene symbol is mapped to a named vector of manufacturer identifiers. The
name represents the gene symbol and the vector contains all manufacturer
identifiers that are found for that symbol. An NA is reported for any
gene symbol that cannot be mapped to any manufacturer identifiers.
This mapping includes ALL gene symbols including those which are already
listed in the SYMBOL map. The SYMBOL map is meant to only list official gene
symbols, while the ALIAS maps are meant to store all used symbols.
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-Sep27
See Also
AnnotationDb-class for use of
the select() interface.
Examples
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
# Convert the object to a list
xx <- as.list(indacALIAS2PROBE)
if(length(xx) > 0){
# Get the probe identifiers for the first two aliases
xx[1:2]
# 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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(indac.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.Dm.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/indac.db/indacALIAS2PROBE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacALIAS2PROBE
> ### Title: Map between Common Gene Symbol Identifiers and Manufacturer
> ### Identifiers
> ### Aliases: indacALIAS2PROBE
> ### Keywords: datasets
>
> ### ** Examples
>
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
>
> ## Bimap interface:
> # Convert the object to a list
> xx <- as.list(indacALIAS2PROBE)
> if(length(xx) > 0){
+ # Get the probe identifiers for the first two aliases
+ xx[1:2]
+ # Get the first one
+ xx[[1]]
+ }
[1] "1000037644"
>
>
>
>
>
> dev.off()
null device
1
>