enrichmentPValue {RVS}R Documentation

enrichment p-value across multiple families and variants

Description

Computes a p-value for all variants seen across all families

Usage

enrichmentPValue(snpMat, famInfo, sharingProbs, threshold = 0)

Arguments

snpMat

SnpMatrix

famInfo

data frame containing pedigree, member, father, mother, sex, affected fields for each sequenced subject

sharingProbs

vector of sharing probabilites, must be a named vector with famid's for each probability

threshold

minimum p-value threshold passed to multipleFamilyPValue

Details

For each variant, the families which have all sequenced subjects sharing the variant and the families which have some sequenced subjects sharing the variant are recorded. All unique (family, variant) pairs are accumulated into a single vector and passed to multipleFamilyPValue

Value

p-value

References

Fu, J., Beaty, T.H., Scott, A.F., Hetmanski, J., Parker, M.M., Bailey-Wilson, J.E., Marazita, M.L., et al. 2017. Whole Exome Association of Rare Deletions in Multiplex Oral Cleft Families. Genetic Epidemiology 41 (1): 61–69. doi:10.1002/gepi.22010.


[Package RVS version 1.16.0 Index]