enrichmentPValue: enrichment p-value across multiple families and variants

In RVS: Computes estimates of the probability of related individuals sharing a rare variant

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.

RVS documentation built on Nov. 8, 2020, 6:57 p.m.