multipleVariantPValue: generalization of multipleFamilyPValue to multiple variants

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

Description

Computes a p-value for each variant sharing pattern across families

Usage

multipleVariantPValue(
  snpMat,
  famInfo,
  sharingProbs,
  minorAllele = NULL,
  filter = NULL,
  alpha = 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
minorAllele	vector specifying the minor allele of each variant
filter	criteria for filtering pvalues
alpha	parameter for filter

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. These values are passed to multipleFamilyPValue

Value

list containing p-values and potential p-values for each variant

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