gwaswloc instance containing information about GWAS in catalog
contextGR
A GRanges instance delimiting the visualization in genomic coordinates
txrefpk
a TxDb package, typically
genesympk
string naming annotationDbi .db package
genome
character tag like 'hg19'
plot.it
logical, if FALSE, just return list
maxmlp
maximum value of -10 log p – winsorization of all larger values is performed,
modifying the contents of Pvalue_mlogp in the elementMetadata for the call
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> library(gwascat)
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
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
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: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
gwascat loaded. Use data(ebicat38) for hg38 coordinates;
data(ebicat37) for hg19 coordinates.
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/gwascat/gwcex2gviz.Rd_%03d_medium.png", width=480, height=480)
> ### Name: gwcex2gviz
> ### Title: Prepare salient components of GWAS catalog for rendering with
> ### Gviz
> ### Aliases: gwcex2gviz
> ### Keywords: graphics
>
> ### ** Examples
>
> args(gwcex2gviz)
function (basegr, contextGR = GRanges(seqnames = "chr17", IRanges(start = 37500000,
width = 1e+06)), txrefpk = "TxDb.Hsapiens.UCSC.hg19.knownGene",
genome = "hg19", genesympk = "Homo.sapiens", plot.it = TRUE,
maxmlp = 25)
NULL
> #gwascat:::.onAttach("", "gwascat")
> data(ebicat37)
> seqlevelsStyle(ebicat37) = "UCSC"
> gwcex2gviz(ebicat37)
'select()' returned 1:1 mapping between keys and columns
>
>
>
>
>
> dev.off()
null device
1
>