Get the scientific evidence for a particular disease-SNP association

This function returns the biomedical evidence that supports the association between a particular SNP and a phenotypic trait.

Usage

getEvidence(variant, diseaseEFO)

Arguments

variant: The SNP ID of a particular variant of interest (e.g. 'rs394581')
diseaseEFO: The EFO identifier of a disease of interest. This can be identified with the function searchDisease()

Value

A tbl_df dataframe containing information about literature evidences for a disease-SNP association.

Note

To retrieve evidences of disease-SNP association, this function makes use of the gwasrapidd package.

References

Ramiro Magno, Ana-Teresa Maia, gwasrapidd: an R package to query, download and wrangle GWAS catalog data, Bioinformatics, Volume 36, Issue 2, January 2020, Pages 649–650, https://doi.org/10.1093/bioinformatics/btz605.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

# \donttest{
# searchDisease("Alzheimer disease")
evidence <- getEvidence("rs2075650", diseaseEFO = "Alzheimer disease")
#> Retrieving biomedical evidence for the association between Alzheimer disease and rs2075650 variant...
#> 112 studies reporting this association were found!
# }