Pathway evidence

GET /pathway

pathway(trait, pval_threshold = 1e-05, mode = c("table", "raw"))

Arguments

trait

A trait name

pval_threshold

P-value threshold

mode

If mode = "table", returns a data frame (a tibble as per tidyverse convention). If mode = "raw", returns a raw response from EpiGraphDB API with minimal parsing done by httr.

Value

Data from GET /pathway

Examples

# \dontrun{
pathway(trait = "Body mass index")
#> # A tibble: 1,100 × 12
#>    gwas.id   gwas.trait      gwas_to_variant.… gwas_to_variant… gwas_to_variant…
#>    <chr>     <chr>                       <dbl>            <dbl>            <dbl>
#>  1 ieu-a-2   Body mass index            0.0803           0.003         2.17e-158
#>  2 ieu-a-2   Body mass index            0.0803           0.003         2.17e-158
#>  3 ieu-a-2   Body mass index            0.0803           0.003         2.17e-158
#>  4 ieu-a-835 Body mass index            0.0818           0.0031        7.52e-153
#>  5 ieu-a-835 Body mass index            0.0818           0.0031        7.52e-153
#>  6 ieu-a-835 Body mass index            0.0818           0.0031        7.52e-153
#>  7 ieu-a-785 Body mass index            0.084            0.0041        4.11e- 94
#>  8 ieu-a-785 Body mass index            0.084            0.0041        4.11e- 94
#>  9 ieu-a-785 Body mass index            0.084            0.0041        4.11e- 94
#> 10 ieu-a-974 Body mass index            0.0774           0.0039        4.87e- 86
#> # … with 1,090 more rows, and 7 more variables:
#> #   gwas_to_variant.samplesize <dbl>, gwas_to_variant.eaf <dbl>,
#> #   variant.name <chr>, gene.name <chr>, protein.uniprot_id <chr>,
#> #   pathway.id <chr>, pathway.name <chr>
# }