This function returns a character vector of Ensembl
biotypes for each supported organism. Mostly for
internal use, but can also be used to list the
biotypes and use some of them to subset initial
genomic regions to be profiled.
Usage
getBiotypes(org)
Arguments
org
One of the supported recoup organisms
See recoup for further information.
Value
A character vector of biotypes.
Author(s)
Panagiotis Moulos
Examples
hg18.bt <- getBiotypes("hg18")
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.
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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(recoup)
Loading required package: GenomicRanges
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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: ggplot2
Loading required package: ComplexHeatmap
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/recoup/getBiotypes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getBiotypes
> ### Title: List default Ensembl biotypes
> ### Aliases: getBiotypes
>
> ### ** Examples
>
> hg18.bt <- getBiotypes("hg18")
>
>
>
>
>
> dev.off()
null device
1
>