README.md

In rondolab/HOPS: The HOPS (HOrizontal Pleiotropy Score) package allows to compute the Horizontal pleiotropy score as described in Jordan et al.

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

rondolab/HOPS documentation built on July 30, 2020, 11:05 a.m.