R: Map between Manufacturer Identifiers and cytogenetic...
indacMAP
R Documentation
Map between Manufacturer Identifiers and cytogenetic maps/bands
Description
indacMAP is an R object that provides mappings between
manufacturer identifiers and cytoband locations.
Details
Each manufacturer identifier is mapped to a vector of cytoband locations. The
vector length may be one or longer, if there are multiple reported
chromosomal locations for a given gene. An NA is reported for
any manufacturer identifiers that cannot be mapped to a cytoband at this time.
Cytogenetic bands for most higher organisms are labeled p1, p2, p3,
q1, q2, q3 (p and q are the p and q arms), etc., counting from the
centromere out toward the telomeres. At higher resolutions, sub-bands
can be seen within the bands. The sub-bands are also numbered from the
centromere out toward the telomere. Thus, a label of 7q31.2 indicates
that the band is on chromosome 7, q arm, band 3, sub-band 1, and
sub-sub-band 2.
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
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:
x <- indacMAP
# Get the probe identifiers that are mapped to any cytoband
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the MAP 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(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/indacMAP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacMAP
> ### Title: Map between Manufacturer Identifiers and cytogenetic maps/bands
> ### Aliases: indacMAP
> ### 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:
> x <- indacMAP
> # Get the probe identifiers that are mapped to any cytoband
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the MAP for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "26B2-26B2"
>
>
>
>
>
> dev.off()
null device
1
>