UKBiobank_ZscoresSubset: Subset of the UK Biobank summary stats.

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

Description

Contains 3 elements 'SNPinfo_UKBB', 'ZscoreMatrix_UKBB' and 'ZscoreCorMatrix_UKBB' to compute the HOPS (HOrizontal Pleiotropy Score) on a subset of 10,000 from the UK Biobank summary stats.

SNP information for the subset of UK Biobank summary stats (10,000 SNPs).

Usage

data("UKBiobank_ZscoresSubset")

Format

SNPinfo_UKBB

data.frame with 10,000 SNPs in rows and information in columns (RS ids, chromosome, position)

ZscoreMatrix_UKBB

data.frame of Z-scores with 10,000 SNPs in row and 372 UK Biobank phenotypes in columns.

ZscoreCorMatrix_UKBB

data.frame of pairwise correlations between Z-scores of the 372 UK Biobank phenotypes.

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