ClusterBurden_WES: ClusterBurden test for burden and position of rare-missense...

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

Description

ClusterBurden test for burden and position of rare-missense variants

Usage

ClusterBurden_WES(
  cases,
  controls,
  case_coverage = NULL,
  control_coverage = NULL,
  cases_ss = NULL,
  controls_ss = NULL,
  cov_threshold = 0.5,
  alternative = "greater",
  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)
cases_ss	sample sizes for cases either a scalar for all genes or a data.table with two columns: symbol, ss
controls_ss	sample sizes for controls either a scalar for all genes or a data.table with two columns: symbol, ss
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

Perform ClusterBurden test across an exome set

Value

A data.table with columns: symbol, ncases, ncontrols, case_ss, control_ss, binp, burdp, clusterburden

Author(s)

Adam Waring - [e-mail]

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