BIN_test_WES: Calculate a p-values from the BIN-test across the whole-exome

In adamwaring/ClusterBurden: Rare variant association utilising burden and positional information.

Description

Calculate a p-values from the BIN-test across the whole-exome

Usage

BIN_test_WES(
  cases,
  controls,
  case_coverage = NULL,
  control_coverage = NULL,
  cov_threshold = 0.5,
  covstats = F,
  messages = T
)

Arguments

cases	case data in format: data.table(aff, symbol, protein_position, ac)
controls	control data in format: data.table(aff, symbol, protein_position, ac)
case_coverage	optional coverage data for cases in format: data.table(symbol, protein_position, over_10)
control_coverage	optional coverage data for controls in format: data.table(symbol, protein_position, over_10)
cov_threshold	threshold at which to exclude a residue position from the analysis (choose 0 to keep all residues)
covstats	include additional coverage information as a column in results?
messages	print messages to the terminal (e.g. how many variants removed by coverage)

Details

This method splits each gene into k = n ^ (2/5) bins where n is the total number of observed variants in the gene. To control for uneven coverage cell counts are adjusted by the reciprocal of the mean 10X coverage across the bin.

Value

Returns a data.table: symbol, p-value, covstats (optional)

Author(s)

Adam Waring - [e-mail]

adamwaring/ClusterBurden documentation built on July 29, 2020, 9:50 p.m.