Query Genotype-Phenotype Association statistics from the UK Biobank Dataset.
Edit run.R file, adding the dbSNP id of the variant of interest. An Example run.R file looks like:
# Make sure to source the PhepideR function
source("PhepideR.R")
notch1 = PhepideR(chromosome = "9",
hg19_position = "139391338",
ref = "C",
alt = "T")An example output looks like:
$meta
# A tibble: 1 x 2
consequence nearest_genes
<chr> <chr>
1 missense_variant NOTCH1
$hits
# A tibble: 1,128 x 12
ac af beta category num_cases num_controls phenocode phenostring pval sebeta trait_is_bad tstat
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> <chr> <chr>
1 13475.3 0.017 2.6 endocrine~ 103 405386 255.11 "Cushing\\u0027s sy~ 1.1e-4 0.67 false 0.073
2 13175.1 0.017 0.56 neurologi~ 1112 395209 331 "Other cerebral deg~ 1.1e-3 0.17 false 0.17
3 11171.7 0.017 -0.44 digestive 1650 334783 564.8 "Abnormal findings ~ 1.6e-3 0.14 false -0.22
4 13505.1 0.017 0.65 endocrine~ 781 405386 252.1 "Hyperparathyroidis~ 1.7e-3 0.21 false 0.14
5 13568.0 0.017 -0.25 sense org~ 4611 402827 386.9 "Dizziness and gidd~ 2.8e-3 0.083 false -0.31
6 13124.1 0.017 0.74 infectiou~ 492 393897 038.2 "Gram positive sept~ 4 e-3 0.26 false 0.1
7 13545.4 0.017 1.3 infectiou~ 163 406301 117.4 "Aspergillosis" 4.9e-3 0.46 false 0.058
8 13563.4 0.017 1.2 symptoms 175 407145 782.6 "Pallor and flushin~ 5.5e-3 0.44 false 0.059
9 13394.7 0.017 -0.62 digestive 617 401525 531.1 "Hemorrhage from ga~ 6.2e-3 0.23 false -0.11
10 13597.1 0.017 0.52 neoplasms 876 407399 227 "Benign neoplasm of~ 6.4e-3 0.19 false 0.12
# ... with 1,118 more rows
$meta refers to the variant type and nearest gene(s), and $hits refers to all the significant regression hits that this variant.
Gagliano Taliun, S.A., VandeHaar, P. et al. Exploring and visualizing large-scale genetic associations by using PheWeb. Nat Genet 52, 550–552 (2020).
Taliun, Daniel, Daniel N. Harris, Michael D. Kessler, Jedidiah Carlson, Zachary A. Szpiech, Raul Torres, Sarah A. Gagliano Taliun, et al. 2021. “Sequencing of 53,831 Diverse Genomes from the NHLBI TOPMed Program.” Nature 590 (7845): 290–99.