R: Create one track of the genomic positions of variants from...
GWAScatalog_UCSC
R Documentation
Create one track of the genomic positions of variants from the GWAS catalog
Description
Create one track of the genomic positions of variants from the NHGRI Catalog of Published Genome-Wide Association Studies using the Gviz bioconductor package
library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 10000
end <- 100000
if(interactive()) {
gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
plotTracks(gwastrack, from = start, to =end)
} else {
data(GWASTrack)
plotTracks(gwastrack, from = start, to =end)
}
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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> 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/GWAScatalog_UCSC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GWAScatalog_UCSC
> ### Title: Create one track of the genomic positions of variants from the
> ### GWAS catalog
> ### Aliases: GWAScatalog_UCSC
> ### Keywords: hplot
>
> ### ** Examples
>
> library("Gviz")
> gen <- "hg38"
> chrom <- "chr2"
> start <- 10000
> end <- 100000
>
> #if(interactive()) {
> gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
> plotTracks(gwastrack, from = start, to =end)
> } else {
Error: unexpected '}' in "}"
Execution halted