Download table containing chromosomal extent and band locations from the UCSC genome browser
Usage
getIdeo(ideoSource)
Arguments
ideoSource
(character) Genome build for data (e.g. mm10).
Details
Uses rtracklayer to retrieve the cytoBandIdeo table from the UCSC genome browser. The cytoBandIdeo table contains chromosomal ideogram information and is used to graph the chromosomal bands in plotOnIdeo(). This table is provided as input to plotOnIdeo(). In the case where the user bins the data, the output of this function can also be used as input to generate bin coordinates for binning the data (see avgByBin()).
Value
(data.frame) ideogram table
Author(s)
Shraddha Pai <Shraddha.Pai@camh.ca>, Jingliang Ren
See Also
avgByBin(),getBins()
Examples
getIdeo("mm9")
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)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(IdeoViz)
Loading required package: Biobase
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
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: RColorBrewer
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdeoViz/getIdeo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getIdeo
> ### Title: Download ideogram table from UCSC
> ### Aliases: getIdeo
>
> ### ** Examples
> getIdeo("mm9")
Error in `genome<-`(`*tmp*`, value = "mm9") :
Failed to set session genome to 'mm9'
Calls: getIdeo -> genome<- -> genome<-
Execution halted