filterUmiObject {umiAnalyzer}

Method for filtering UMIexperiment and sample objects

Description

Method for filtering UMIexperiment and sample objects

Usage

filterUmiObject(
  object,
  name = "default",
  minDepth = 3,
  minCoverage = 100,
  minFreq = 0,
  minCount = 0
)

Arguments

object

Requires a UMI sample or UMI experiment object.

name

String. Name of the filter. Default is "default".

minDepth

Consensus depth to analyze. Default is 3.

minCoverage

Minimum coverage required for amplicons. Default is 1.

minFreq

Minimum variant allele frequency to keep. Default is 0.

minCount

Minimum variant allele count to keep. Default is 3.

Value

A UMI sample or UMI experiment object.

Examples

library(umiAnalyzer)

main = system.file('extdata', package = 'umiAnalyzer')

samples <- list.dirs(path = main, full.names = FALSE, recursive = FALSE)

simsen <- createUmiExperiment(experimentName = 'simsen',mainDir = main,sampleNames = samples)

simsen <- filterUmiObject(simsen)