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README.md

nanostringr

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An R Package for quality assurance checking, normalization and batch effects adjustments of NanoString data suitable for single sample processing. This is the companion R package for the paper "Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction", published in PLOS ONE.

Installation

To install this package, use devtools:

# install.packages(devtools)
devtools::install_github("OVCARE/nanostringr", build_vignettes = TRUE)

Dependencies

Please note that the package CHL26predictor is needed to run the Hodgkin Lymphoma predictive model shown in the vignette.

Overview

To see the full list of exported functions:

library(nanostringr)
ls("package:nanostringr")

A quick overview of the key functions:

  • NanoStringQC: Computes quality assurance metrics.
  • HKnorm: Performs log (base 2) transformation and normalization to Housekeeping Genes
  • refMethod: Performs batch effect correction using the reference-based strategy

A vignette that reproduces most of the analyses in the paper is included. The vignettes can be accessed in R using

browseVignettes("nanostringr")