Currently GWAS direction made a lot of literature, but does not have a very well-R package for the pooled data from these documents.
The next recommendation is the latest publication of this summary R GWAS data packets. Looked fully functional, but the data is not included is complete.
The following specific to talk about.
Mounted on R
install.packages("remotes")
remotes::install_github("ramiromagno/gwasrapidd")
Is there a query published an article about autoimmune diseases
library(gwasrapidd)
my_studies <- get_studies(efo_trait = 'autoimmune disease')
Queries article published number of autoimmune diseases
n(my_studies)
Get articles published in autoimmune diseases ID
my_studies@studies$study_id
Queries published an article titled autoimmune diseases
my_studies@publications$title
View article published in autoimmune diseases of interface information pubmed
open_in_pubmed(my_studies@publications$pubmed_id)
SNP obtain information related literature published Height
my_associations <- get_associations(study_id = my_studies@studies$study_id)
P values less than query site of 1e-6
dplyr::filter(my_associations@associations, pvalue < 1e-6) %>% # Filter by p-value
tidyr::drop_na(pvalue) %>%
dplyr::pull(association_id) -> association_ids # Extract column association_id
Extracting significant information signal site
my_associations2 <- my_associations[association_ids]
A significant number of display signal site
n(my_associations2)
Showed significant sites signal RS ID, risk allele, the frequency
my_associations2@risk_alleles[c('variant_id', 'risk_allele', 'risk_frequency')] %>%
print(n = Inf)
Get document containing site rs12752552
s2 <- get_studies(variant_id = 'rs12752552')
Test it, minus the advantage of a lot of information retrieval work, the disadvantage is that this newly developed package soon, not enough information is complete
For more details see gwasrapidd
参考文献：Magno R, Maia A T. gwasrapidd: an R package to query, download and wrangle GWAS Catalog data[J]. bioRxiv, 2019: 643940.