library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 100000
end <- 10000000
if(interactive()) {
clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
plotTracks(clinVariant, from = start, to =end)
}else{
data(clinVarMaintrack)
plotTracks(clinVariant, from = start, to =end)
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(coMET)
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych
Attaching package: 'psych'
The following object is masked from 'package:IRanges':
reflect
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/coMET/ClinVarMain_UCSC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ClinVarMain_UCSC
> ### Title: Create one track of the genomic positions of variants from the
> ### ClinVar database (variants only)
> ### Aliases: ClinVarMain_UCSC
> ### Keywords: hplot
>
> ### ** Examples
>
> library("Gviz")
> gen <- "hg38"
> chrom <- "chr2"
> start <- 100000
> end <- 10000000
>
> #if(interactive()) {
> clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
> plotTracks(clinVariant, from = start, to =end)
> }else{
Error: unexpected '}' in "}"
Execution halted