findConsensusReads {umiAnalyzer}

Find consensus reads A function to analyze consensus read tables generated with parseBamFiles or a UMIexperiment object containing reads.

Description

Find consensus reads A function to analyze consensus read tables generated with parseBamFiles or a UMIexperiment object containing reads.

Usage

findConsensusReads(
  object,
  consDepth = 0,
  groupBy = c("none", "sample", "position", "both"),
  pattern = NULL
)

Arguments

object

Either a tibble generated with parseBamFiles or a UMIexperiment object

consDepth

Minimum consensus depth to keep. Default is 0.

groupBy

Should data be grouped by position, sample, both or not at all.

pattern

Regular expression

Value

A data table

Examples

library(umiAnalyzer)
main <- system.file("extdata", package = "umiAnalyzer")
simsen <- createUmiExperiment(main, importBam = TRUE)

reads <- findConsensusReads(simsen)
reads