remove_uncovered_residues: Exclude residue positions from a dataset based on coverage...

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

Description

Exclude residue positions from a dataset based on coverage files

Usage

remove_uncovered_residues(
  dataset,
  case_coverage,
  control_coverage,
  cov_threshold,
  messages
)

Arguments

dataset	case-control data.table with at least columns: symbol and protein_position
case_coverage	optional coverage data for cases in format: data.table(symbol, index, over_10)
control_coverage	optional coverage data for controls in format: data.table(symbol, index, over_10)
cov_threshold	threshold at which to exclude a residue position from the analysis (choose 0 to keep all residues)
messages	print messages to the terminal (e.g. how many variants removed by coverage)

Details

Variant residues are removed from both cases and controls if they have low coverage in either case or control coverage. These positions are also removed from the coverage files to make downstream esimation of regional coverage accurate in light of variants removed.

Author(s)

Adam Waring - [e-mail]

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