Repository files navigation

Tools for analyzing sequencing data containing uniquemolecular identifiers generated by UMIErrorCorrect(https://github.com/stahlberggroup/umierrorcorrect). The packageallows merging of multiple samples into a single UMIexperiment object whichcan be easily manipulated using build-in functions to generate tabular andgraphical output. The package includes a shiny app with a graphicaluser interface for data exploration and generating plots and reportdocuments.

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

browseVignettes('umiAnalyzer')

For a version history/changelog, please see theNEWS file.

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

Install the current stable version from CRAN:

# from CRANinstall.packages('umiAnalyzer')

Alternatively, you can download the stable version or the latest developmentversion from GitHub using devtools:

# get the current stable version from github using the devtools package:devtools::install_github('sfilges/umiAnalyzer')# get the latest development version:devtools::install_github('sfilges/umiAnalyzer',ref='devel')

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

umiAnalyzer::runUmiVisualizer()

Define a variable containing the path to the directory with all the UMIErrorCorrectoutput folders belonging to your experiment. umiAnalyzer comes with raw test datagenerated 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 createas 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)bc_hist<- BarcodeFamilyHistogram(reads)bc_histqc_plot<- QCplot(simsen)qc_plotsimsen<- filterUmiObject(simsen)myfilter<- getFilteredData(simsen)myfilteramplicon_plot<- AmpliconPlot(simsen)amplicon_plot