HOPS (HOrizontal Pleiotropy Score)

The HOPS package allows to compute the horizontal pleiotropy score (HOrizontal Pleiotropy Score) from summary statistics. The package includes a shiny visualization tool to visualize and download the full set of HOPS results computed using UK Biobank summary statistics

Reference

Daniel Jordan*, Marie Verbanck* and Ron Do. HOPS: a quantitative score reveals pervasive horizontal pleiotropy in human genetic variation is driven by extreme polygenicity of human traits and diseases. Genome Biology 20, 222 (2019).

https://doi.org/10.1186/s13059-019-1844-7

1. Install and load PleiotropyScore

To install the latest development builds directly from GitHub, run this instead:

if (!require("devtools")) { install.packages("devtools") } else {}
devtools::install_github("rondolab/HOPS")

Load HOPS

library(HOPS)

2. Example: run the HOPS on a subset of the UK Biobank summary stats

# Load a subset of the UK Biobank summary statistics
data(UKBiobank_ZscoresSubset)
# Apply the whitening procedure
ZscoreMatrixWhitened_UKBB <- GetWhitenedZscores(ZscoreMatrix = ZscoreMatrix_UKBB, ZscoreCorMatrix = ZscoreCorMatrix_UKBB)
# Get the LD-corrected HOPS
HOPS_UKBB <- GetHOPS(ZscoreWhitenedMatrix = ZscoreMatrixWhitened_UKBB, RSids = SNPinfo_UKBB$SNPid, LDCorrected = TRUE, POLYGENICITYCorrected = FALSE, GlobalTest = TRUE)
# Results
GlobalTest_UKBB <- HOPS_UKBB[[1]]
HOPS_UKBB <- HOPS_UKBB[[2]]

3. Visualize and download the full set of HOPS results in the UK Biobank

# To run the HOPS results interface
RunHOPSApp()

The full set of results is also directly downloadable here:

https://github.com/rondolab/HOPS/raw/master/inst/shiny-examples/HOPSApp/www/ScoresUKbbSAIGE_AllSNPs_LDTheo.txt.tar.gz

The Zscore correlation matrix for the 372 UK Biobank phenotypes is directly downloadable here: https://github.com/rondolab/HOPS/raw/master/inst/shiny-examples/HOPSApp/www/UkBiobank_Zscore_CorrelationMat.xlsx