vignettes/OpenGWAS.Rmd
OpenGWAS.RmdMungeSumstats now offers high throughput query and import functionality to data from the MRC IEU Open GWAS Project.
#### Search for datasets ####
metagwas <- MungeSumstats::find_sumstats(traits = c("parkinson","alzheimer"),
min_sample_size = 1000)
head(metagwas,3)
ids <- (dplyr::arrange(metagwas, nsnp))$id ## id trait group_name year author
## 1 ieu-a-298 Alzheimer's disease public 2013 Lambert
## 2 ieu-b-2 Alzheimer's disease public 2019 Kunkle BW
## 3 ieu-a-297 Alzheimer's disease public 2013 Lambert
## consortium
## 1 IGAP
## 2 Alzheimer Disease Genetics Consortium (ADGC), European Alzheimer's Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer's Disease Consortium (GERAD/PERADES),
## 3 IGAP
## sex population unit nsnp sample_size build
## 1 Males and Females European log odds 11633 74046 HG19/GRCh37
## 2 Males and Females European NA 10528610 63926 HG19/GRCh37
## 3 Males and Females European log odds 7055882 54162 HG19/GRCh37
## category subcategory ontology mr priority pmid sd
## 1 Disease Psychiatric / neurological NA 1 1 24162737 NA
## 2 Binary Psychiatric / neurological NA 1 0 30820047 NA
## 3 Disease Psychiatric / neurological NA 1 2 24162737 NA
## note ncase
## 1 Exposure only; Effect allele frequencies are missing; forward(+) strand 25580
## 2 NA 21982
## 3 Effect allele frequencies are missing; forward(+) strand 17008
## ncontrol N
## 1 48466 74046
## 2 41944 63926
## 3 37154 54162You can supply import_sumstats() with a list of as many
OpenGWAS IDs as you want, but we’ll just give one to save time.
datasets <- MungeSumstats::import_sumstats(ids = "ieu-a-298",
ref_genome = "GRCH37")By default, import_sumstats results a named list where
the names are the Open GWAS dataset IDs and the items are the respective
paths to the formatted summary statistics.
print(datasets)## $`ieu-a-298`
## [1] "/tmp/RtmpI3qdKJ/ieu-a-298.tsv.gz"You can easily turn this into a data.frame as well.
results_df <- data.frame(id=names(datasets),
path=unlist(datasets))
print(results_df)## id path
## ieu-a-298 ieu-a-298 /tmp/RtmpI3qdKJ/ieu-a-298.tsv.gzOptional: Speed up with multi-threaded download via axel.
datasets <- MungeSumstats::import_sumstats(ids = ids,
vcf_download = TRUE,
download_method = "axel",
nThread = max(2,future::availableCores()-2))See the Getting started vignette for more information on how to use MungeSumstats and its functionality.
utils::sessionInfo()## R Under development (unstable) (2022-12-07 r83413)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MungeSumstats_1.7.10 BiocStyle_2.27.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.0 dplyr_1.0.10
## [3] blob_1.2.3 filelock_1.0.2
## [5] R.utils_2.12.2 Biostrings_2.67.0
## [7] bitops_1.0-7 fastmap_1.1.0
## [9] RCurl_1.98-1.9 BiocFileCache_2.7.1
## [11] VariantAnnotation_1.45.0 GenomicAlignments_1.35.0
## [13] XML_3.99-0.13 digest_0.6.31
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