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

pathway(trait = "Body mass index")
#> # A tibble: 88 x 11 #> gwas.id gwas.trait gwas_to_variant… gwas_to_variant… gwas_to_variant… #> <chr> <chr> <dbl> <dbl> <dbl> #> 1 ieu-a-2 Body mass… 0.0803 0.00300 0. #> 2 ieu-a-… Body mass… 0.0840 0.00410 0. #> 3 ieu-a-… Body mass… 0.0818 0.00310 0. #> 4 ieu-a-… Body mass… 0.0774 0.00390 0. #> 5 ieu-a-… Body mass… 0.0850 0.00640 1.14e-40 #> 6 ieu-a-… Body mass… 0.0760 0.00630 6.00e-34 #> 7 ieu-a-2 Body mass… -0.0416 0.0037 6.66e-30 #> 8 ieu-a-… Body mass… -0.0414 0.00380 5.56e-28 #> 9 ieu-a-… Body mass… 0.0334 0.00310 2.66e-26 #> 10 ieu-a-2 Body mass… 0.0311 0.00300 3.45e-25 #> # … with 78 more rows, and 6 more variables: gwas_to_variant.samplesize <dbl>, #> # variant.name <chr>, gene.name <chr>, protein.uniprot_id <chr>, #> # pathway.reactome_id <chr>, pathway.name <chr>