Package: gwascat 2.39.0

VJ Carey

gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Represent and model data in the EMBL-EBI GWAS catalog.

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gwascat.pdf |gwascat.html✨
gwascat/json (API)
NEWS

# Install 'gwascat' in R:

install.packages('gwascat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

ebicat_2020_04_30 - Serialized gwaswloc instance from april 30 2020, sample of 50000 records
efo.obo.g - Convert a typical OBO text file to a graphNEL instance
g17SM - SnpMatrix instance from chr17
gg17N - Genotype matrix from chr17 1000 genomes
gr6.0_hg38 - Image of locon6 in GRanges, lifted over to hg38
gw6.rs_17 - Character vector of rs numbers for SNP on chr17
gwastagger - GRanges with LD information on 9998 SNP
locon6 - Location data for 10000 SNP
low17 - SnpMatrix instance from chr17
si.hs.37 - Seqinfo for GRCh37
si.hs.38 - Seqinfo for GRCh38

On BioConductor:gwascat-2.39.0(bioc 3.21)gwascat-2.38.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genetics

6.07 score 2 packages 108 scripts 1.1k downloads 4 mentions 18 exports 99 dependencies

Last updated 25 days agofrom:a659d472cd. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 06 2024
R-4.5-win	WARNING	Nov 06 2024
R-4.5-linux	WARNING	Nov 06 2024
R-4.4-win	WARNING	Nov 06 2024
R-4.4-mac	NOTE	Nov 06 2024
R-4.3-win	WARNING	Nov 06 2024
R-4.3-mac	NOTE	Nov 06 2024

Exports:as_GRanges bindcadd_snv get_cached_gwascat getRsids getTraits gwascat_from_AHub gwcat_snapshot gwcex2gviz ldtagr locs4trait makeCurrentGwascat obo2graphNEL process_gwas_dataframe riskyAlleleCount subsetByChromosome subsetByTraits topTraits traitsManh

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome cachem cli clipr codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue hms httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RCurl readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow snpStats SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 VariantAnnotation vctrs vroom withr XML XVector yaml zlibbioc

GWAS catalog: Phenotypes systematized by the experimental factor ontology

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromgwascatOnt.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2020-05-02
Started: 2015-08-03

gwascat: structuring and querying the NHGRI GWAS catalog

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromgwascat.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2022-08-09
Started: 2020-05-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
extractor for gwaswloc	[,gwaswloc,ANY,ANY,ANY-method
produce a GRanges from gwascat tibble	as_GRanges
bind CADD scores of Kircher et al. 2014 to a GRanges instance	bindcadd_snv
return TRUE if all named SNPs with locations in both the SNPlocs package and the gwascat agree	chklocs
serialized gwaswloc instance from april 30 2020, sample of 50000 records	ebicat_2020_04_30
SnpMatrix instance from chr17	g17SM
use BiocFileCache to retrieve and keep an image of the tsv file distributed by EBI	get_cached_gwascat
generic snp name retrieval	getRsids
specific snp name retrieval	getRsids,gwaswloc-method
generic trait retrieval	getTraits
specific trait retrieval	getTraits,gwaswloc-method
genotype matrix from chr17 1000 genomes	gg17N
image of locon6 in GRanges, lifted over to hg38	gr6.0_hg38
character vector of rs numbers for SNP on chr17	gw6.rs_17
grab an image of EBI GWAS catalog from AnnotationHub	gwascat_from_AHub
GRanges with LD information on 9998 SNP	gwastagger
container for gwas hit data and GRanges for addresses	gwaswloc-class
use AnnotationHub snapshot as basis for gwaswloc structure creation	gwcat_snapshot
Prepare salient components of GWAS catalog for rendering with Gviz	gwcex2gviz
expand a list of variants by including those in a VCF with LD exceeding some threshold; uses snpStats ld()	ldtagr
location data for 10000 SNP	locon6
get locations for SNP affecting a selected trait	locs4trait
SnpMatrix instance from chr17	low17
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.	makeCurrentGwascat
convert a typical OBO text file to a graphNEL instance (using Term elements)	efo.obo.g node2uri obo2graphNEL uri2node
convert GWAS catalog data.frame to gwaswloc, a GRanges extension with simple show method	process_gwas_dataframe
given a matrix of subjects x SNP calls, count number of risky alleles	riskyAlleleCount
Seqinfo for GRCh37	si.hs.37
Seqinfo for GRCh38	si.hs.38
generic trait subsetting	subsetByChromosome
specific trait subsetting	subsetByChromosome,gwaswloc-method
generic trait subsetting	subsetByTraits
specific trait subsetting	subsetByTraits,gwaswloc-method
operations on GWAS catalog	topTraits
use ggbio facilities to display GWAS results for selected traits in genomic coordinates	traitsManh