HOPS-package: The HOPS (HOrizontal Pleiotropy Score) package allows to...

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

Description

The HOPS (HOrizontal Pleiotropy Score) package allows to compute the horizontal pleiotropy score as described in Jordan et al. The full set of pleiotropy scores computed on the UK Biobank summary statistics is available through the package using the function RunHOPSApp().

Details

The DESCRIPTION file: The HOPS (HOrizontal Pleiotropy Score) package allows to compute the horizontal pleiotropy score as described in Jordan et al. The full set of pleiotropy scores computed on the UK Biobank summary statistics is available through the package using the function RunHOPSApp().

Index: This package was not yet installed at build time.
The HOPS package allows to compute the HOPS (HOrizontal Pleiotropy Score) as described in Jordan et al. The full set of HOPS computed on the UK Biobank summary statistics is available through the package using the function RunHOPSApp().

Author(s)

Marie Verbanck Maintainer: <[e-mail]>

References

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).

Examples

	################# 1- 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]]

	################# 2- visualize the full set of HOPS results in the UK Biobank #################
	# To run the HOPS results interface
	RunHOPSApp()

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