umiAnalyzer (version 1.0.0)

parseBamFiles: Function to parse bam files

Description

Function to parse bam files

Usage

parseBamFiles(mainDir, sampleNames = NULL, consDepth = 0, as.shiny = FALSE)

Arguments

mainDir

Directory containing UMIErrorCorrect output folders.

sampleNames

A list of sample names.

consDepth

Only retain consensus reads of at least cons.depth. Default is 0.

as.shiny

Set to TRUE if run within a shiny::withProgress environment

Value

A data table

Examples

# NOT RUN {
library(umiAnalyzer)
main <- system.file("extdata", package = "umiAnalyzer")
simsen <- createUmiExperiment(main)

reads <- parseBamFiles(main, consDepth = 10)
# }
# NOT RUN {
# }