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.
To install this package, use
# install.packages(devtools) devtools::install_github("OVCARE/nanostringr", build_vignettes = TRUE)
Please note that the package CHL26predictor is needed to run the Hodgkin Lymphoma predictive model shown in the vignette.
To see the full list of exported functions:
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