R: Create one track of the genomic positions of variants from...
GAD_UCSC
R Documentation
Create one track of the genomic positions of variants from the Genetic Association Database (GAD)
Description
Create one track of the genomic positions of variants from the Genetic Association Database (GAD) (archive of human genetic association studies of complex diseases and disorders) using the Gviz bioconductor package
Usage
GAD_UCSC(gen, chr, start, end, showId=FALSE)
Arguments
gen
the name of the genome. Data is not currently available for GRCh38 (hg38).
chr
the chromosome of interest
start
the first position in the region of interest (the smallest value)
end
the last position in the region of interest (the largest value)
library("Gviz")
gen2 <- "hg19"
chrom2 <- "chr2"
start2 <- 38290160
end2 <- 38303219
if(interactive()) {
gadtrack<-GAD_UCSC(gen=gen2 ,chr=chrom2 ,start=start2 ,end=end2)
plotTracks(gadtrack, from = start2, to =end2)
} else {
data(gadtrack)
plotTracks(gadtrack, from = start2, to =end2)
}
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.
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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(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/GAD_UCSC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GAD_UCSC
> ### Title: Create one track of the genomic positions of variants from the
> ### Genetic Association Database (GAD)
> ### Aliases: GAD_UCSC
> ### Keywords: hplot
>
> ### ** Examples
>
> library("Gviz")
> gen2 <- "hg19"
> chrom2 <- "chr2"
> start2 <- 38290160
> end2 <- 38303219
>
> #if(interactive()) {
> gadtrack<-GAD_UCSC(gen=gen2 ,chr=chrom2 ,start=start2 ,end=end2)
Error in `genome<-`(`*tmp*`, value = "hg19") :
Failed to set session genome to 'hg19'
Calls: GAD_UCSC ... .doCache -> eval -> eval -> eval -> genome<- -> genome<-
Execution halted