makeCurrentGwascat: read NHGRI GWAS catalog table and construct associated...
In gwascat: representing and modeling data in the EMBL-EBI GWAS catalog
Description
Usage
Arguments
Value
Author(s)
Examples
Description
read NHGRI GWAS catalog table and construct associated GRanges instance
records for which clear genomic position cannot be determined are dropped
from the ranges instance
an effort is made to use reasonable data types for GRanges metadata, so some
qualifying characters such as (EA) in Risk allele frequency field will
simply be omitted during coercion of contents of that field to numeric.
Usage
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makeCurrentGwascat(
table.url = "http://www.ebi.ac.uk/gwas/api/search/downloads/alternative",
fixNonASCII = TRUE,
genome = "GRCh38",
withOnt = TRUE
)
Arguments
table.url
string identifying the .txt file curated at EBI/EMBL
fixNonASCII
logical, if TRUE, non-ASCII characters as identified by
iconv will be replaced by asterisk
genome
character string: 'GRCh38' is default and yields current image
as provided by EMBL/EBI; 'GRCh37' yields a realtime liftOver to hg19
coordinates, via AnnotationHub storage of the chain files. Any other value
yields an error.
withOnt
logical indicating whether 'alternative' (ontology-present,
includes repetition of loci with one:many ontological mapping) or 'full'
(ontology-absent, one record per locus report) version of distributed table
Value
a GRanges instance
Author(s)
VJ Carey
Examples
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# if you have good internet access
if (interactive()) {
newcatr = makeCurrentGwascat()
newcatr
}
gwascat documentation built on Nov. 8, 2020, 11:08 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
read NHGRI GWAS catalog table and construct associated GRanges instance records for which clear genomic position cannot be determined are dropped from the ranges instance an effort is made to use reasonable data types for GRanges metadata, so some qualifying characters such as (EA) in Risk allele frequency field will simply be omitted during coercion of contents of that field to numeric.
Usage
1 2 3 4 5 6 | makeCurrentGwascat(
table.url = "http://www.ebi.ac.uk/gwas/api/search/downloads/alternative",
fixNonASCII = TRUE,
genome = "GRCh38",
withOnt = TRUE
)
|
Arguments
table.url |
string identifying the .txt file curated at EBI/EMBL |
fixNonASCII |
logical, if TRUE, non-ASCII characters as identified by iconv will be replaced by asterisk |
genome |
character string: 'GRCh38' is default and yields current image as provided by EMBL/EBI; 'GRCh37' yields a realtime liftOver to hg19 coordinates, via AnnotationHub storage of the chain files. Any other value yields an error. |
withOnt |
logical indicating whether 'alternative' (ontology-present, includes repetition of loci with one:many ontological mapping) or 'full' (ontology-absent, one record per locus report) version of distributed table |
Value
a GRanges instance
Author(s)
VJ Carey
Examples
1 2 3 4 5 | # if you have good internet access
if (interactive()) {
newcatr = makeCurrentGwascat()
newcatr
}
|
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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