GetHOPS: Get HOrizontal Pleiotropy Score (HOPS).

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

Description

Allows to compute the HOrizontal Pleiotropy Score (HOPS) from the matrix of whitened Zscores.

Usage

GetHOPS(ZscoreWhitenedMatrix, RSids, LDCorrected = FALSE, POLYGENICITYCorrected = FALSE, NBSim = 25, GlobalTest = FALSE)

Arguments

ZscoreWhitenedMatrix	a data.frame of Z-scores with SNPs in rows and traits in columns. Careful no to include any column with SNP ids, SNP ids should be specified using the argument 'RSids', only Zscores should be included.
RSids	Character vector of RS ids, in the same order as rows of ZscoreWhitenedMatrix, used to match the SNPs to LD scores for the LD-corrected HOPS (in case argument 'LDCorrected' set to TRUE). RS ids must be in build 38.
LDCorrected	Boolean, TRUE if LD-corrected HOPS should be computed. Default is TRUE.
POLYGENICITYCorrected	Boolean, TRUE if polygenicity-corrected HOPS should be computed. Default is FALSE.
NBSim	Integer, Number of permutations to compute empirical P-values in case POLYGENICITYCorrected is set to TRUE. Default is 25.
GlobalTest	Boolean, if TRUE the results of the global test testing for a shift in the distribution of the HOPS for all SNPs. Default is FALSE.

Value

GlobalTest	if 'GlobalTest' set to TRUE, P-value of the global test.
HOPS	data.frame containing the HOrizontal Pleiotropy Score (HOPS) for all SNPs

Author(s)

Marie Verbanck

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

    # 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]]

rondolab/PleiotropyScore documentation built on Aug. 4, 2020, 2:13 a.m.