GetWhitenedZscores: Get Whitened Z-scores

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

Description

Get whitened Z-scores from a matrix of Z-scores (SNPs in rows, traits in columns) and a correlation matrix between traits.

Usage

    GetWhitenedZscores(ZscoreMatrix, ZscoreCorMatrix = NULL)

Arguments

ZscoreMatrix	data.frame of Z-scores with SNPs in rows and traits in columns.
ZscoreCorMatrix	data.frame of pairwise correlations between traits based on Z-scores. Usually computed using a pruned set of SNPs, see function 'GetCorrelationMatrix()'. If set to NULL, the full set of SNPs included in ZscoreMatrix is used. Default is NULL.

Value

ZscoreWhitenedMatrix

data.frame of the same size as 'ZscoreMatrix' composed of whitened Z-scores.

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).

See Also

GetCorrelationMatrix

Examples

    data(UKBiobank_ZscoresSubset)
    ZscoreMatrixWhitened_UKBB <- GetWhitenedZscores(ZscoreMatrix = ZscoreMatrix_UKBB, ZscoreCorMatrix = ZscoreCorMatrix_UKBB)

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