bayesTest: Bayes test of excess variant frequency with CADD-based prior

In pbreheny/epcot: Exome-sequencing Paired Case-Only Tests

Description

Bayes test of excess variant frequency with CADD-based prior

Usage

bayesTest(
  N.pair,
  N.trio,
  vData,
  cutoff = 0.2,
  ceiling = 2000,
  floor = 0.01,
  rate = 0.5,
  Q = 100
)

Arguments

N.pair	Matrix of 0/1/2 counts for sister pairs
N.trio	Matrix of 0/1/2/3 counts for sister trios
vData	data.table of variant info (ExAC frequencies and CADD scores)
cutoff	Exclude variants with ExAC frequencies above this cutoff
ceiling	Ceiling for prior
floor	Floor for prior
rate	Decay rate for prior
Q	Number of null simulations to run for q value calculation

Examples

N2 <- epcot_example$N2
N3 <- epcot_example$N3
vData <- epcot_example$vData
res <- bayesTest(N2, N3, vData)
head(res[order(res$FDR),])

pbreheny/epcot documentation built on June 18, 2021, 7:46 a.m.