gwcex2gviz: Prepare salient components of GWAS catalog for rendering with...
In vjcitn/gwascat: representing and modeling data in the EMBL-EBI GWAS catalog
Description
Usage
Arguments
Examples
Description
Prepare salient components of GWAS catalog for rendering with Gviz
Usage
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gwcex2gviz(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)
Arguments
basegr
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
Examples
1
2
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5
args(gwcex2gviz)
#gwascat:::.onAttach("", "gwascat")
data(ebicat37)
seqlevelsStyle(ebicat37) = "UCSC"
gwcex2gviz(ebicat37)
vjcitn/gwascat documentation built on May 5, 2019, 7:59 p.m.
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Description Usage Arguments Examples
Description
Prepare salient components of GWAS catalog for rendering with Gviz
Usage
1 2 3 4 5 | gwcex2gviz(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)
|
Arguments
basegr |
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 |
Examples
1 2 3 4 5 | args(gwcex2gviz)
#gwascat:::.onAttach("", "gwascat")
data(ebicat37)
seqlevelsStyle(ebicat37) = "UCSC"
gwcex2gviz(ebicat37)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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