illuminaHumanv4CHR is an R object that provides mappings between a
manufacturer identifier and the chromosome that contains the gene of interest.
Details
Each manufacturer identifier maps to a vector of chromosomes. Due to
inconsistencies that may exist at the time the object was built,
the vector may contain more than one chromosome (e.g., the identifier may map
to more than one chromosome). If the chromosomal location is unknown,
the vector will contain an NA.
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
Examples
x <- illuminaHumanv4CHR
# Get the probe identifiers that are mapped to a chromosome
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the CHR 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)
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(illuminaHumanv4.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/illuminaHumanv4.db/illuminaHumanv4CHR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv4CHR
> ### Title: Map Manufacturer IDs to Chromosomes
> ### Aliases: illuminaHumanv4CHR
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaHumanv4CHR
> # Get the probe identifiers that are mapped to a chromosome
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the CHR for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "6"
>
>
>
>
>
> dev.off()
null device
1
>