This function connects to the EBI's Biomart service using
the package biomaRt and downloads annotation elements
(gene co-ordinates, exon co-ordinates, gene
identifications, biotypes etc.) for each of the supported
organisms. See the help page of recoup
for a list of supported organisms. The function downloads
annotation for an organism genes or exons. It also uses
the UCSC public database connection API to download UCSC
and RefSeq annotations.
the organism for which to download
annotation. Check the main recoup
help page for details on supported organisms.
type
either "gene" or "exon".
refdb
the online source to use to fetch
annotation. It can be "ensembl" (default),
"ucsc" or "refseq". In the later two
cases, an SQL connection is opened with the UCSC
public databases.
rc
fraction (0-1) of cores to use in a multicore
system. It defaults to NULL (no parallelization).
It is used in the case of type="exon" to process
the return value of the query to the UCSC Genome
Browser database.
Value
A data frame with the canonical (not isoforms!) genes or
exons of the requested organism. When
type="genes", the data frame has the following
columns: chromosome, start, end, gene_id, gc_content,
strand, gene_name, biotype. When type="exon" the
data frame has the following columns: chromosome, start,
end, exon_id, gene_id, strand, gene_name, biotype. The
gene_id and exon_id correspond to Ensembl gene and exon
accessions respectively. The gene_name corresponds to
HUGO nomenclature gene names.
Note
The data frame that is returned contains only "canonical"
chromosomes for each organism. It does not contain
haplotypes or random locations and does not contain
chromosome M.
Author(s)
Panagiotis Moulos
Examples
mm9.genes <- getAnnotation("mm9","gene")
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(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/getAnnotation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getAnnotation
> ### Title: Annotation downloader
> ### Aliases: getAnnotation
>
> ### ** Examples
>
> mm9.genes <- getAnnotation("mm9","gene")
>
>
>
>
>
> dev.off()
null device
1
>