filterUmiObject: Method for filtering UMIexperiment and sample objects

In umiAnalyzer: Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

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)

umiAnalyzer documentation built on Nov. 25, 2021, 9:07 a.m.