umiAnalyzer 1.0.0

Tools for analyzing sequencing data containing unique molecular identifiers generated by UMIErrorCorrect (https://github.com/stahlberggroup/umierrorcorrect). The package allows merging of multiple samples into a single UMIexperiment object which can be easily manipulated using build-in functions to generate tabular and graphical output. The package includes a shiny app with a graphical user interface for data exploration and generating plots and report documents.

This README serves as a basic introduction, for more detailed information and examples read the wiki pages on GitHub (https://github.com/sfilges/umiAnalyzer/wiki) or the R vignette using:

browseVignettes('umiAnalyzer')

For a version history/changelog, please see the NEWS file.

Requirements

• R (>= 4.1.0), which can be downloaded and installed via The Comprehensive R Archive Network CRAN.
• Installation from R using install_github requires the devtools package

Installation

Install the current stable version from CRAN or GitHub or the latest development version from GitHub.

# from CRAN (not supported yet)
#install.packages('umiAnalyzer')

# Current stable version from github using the devtools package:
devtools::install_github('sfilges/umiAnalyzer')

# Latest development version from github:
devtools::install_github('sfilges/umiAnalyzer', ref = 'devel')

Running the visualization app

Run the following command in the R console to start the app:

umiAnalyzer::runUmiVisualizer()

Using the R package in your own scripts

How to make build your own UMIexperiment object

Define a variable containing the path to the directory with all the UMIErrorCorrect output folders belonging to your experiment. umiAnalyzer comes with raw test data generated with UMIErrorCorrect that you can import if you don't have any of your own.

Call the createUmiExperiment to create your UMIexperiment object.

The UMIexperiment object always maintains your raw data, however you can create as many filters as you like, which will be saved as separate objects to access. You can filter the consensus table of UMIexperiment object with filterUMIobject. The only mandatory arguments are the object to be filtered and a user defined name. You can use that name to retrieve a filtered table using getFilter.

library(umiAnalyzer)

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

simsen <- createUmiExperiment(main)

reads <- parseBamFiles(main, consDepth = 10)

plotFamilyHistogram(reads)

simsen <- generateQCplots(simsen)

simsen <- filterUmiObject(simsen)

myfilter <- getFilteredData(simsen)
myfilter

simsen <- generateAmpliconPlots(simsen)