CHL26predictor

An R Package for the Classical Hodgkin Lymphoma (CHL) 26 Gene Overall Survival Predictor. This is the companion R package for the predictor that has been published.

• Scott, D. W., Chan, F. C., Hong, F., Rogic, S., Tan, K. L., Meissner, B., et al. (2013). Gene expression-based model using formalin-fixed paraffin-embedded biopsies predicts overall survival in advanced-stage classical Hodgkin lymphoma. J Clin Oncol, 31(6), 692–700. doi:10.1200/JCO.2012.43.4589

Installation

The preferred way to install this package is through conda:

conda install -c fongchun chl26predictor

Alternatively, one can install this package, using devtools:

devtools::install_github("LCR-BCCRC/CHL26predictor")

Suggested Dependencies

This package suggests the installation of the NanoStringNorm R package for access to some additional (but non-essential) functions (e.g. convert_RCC_to_mat). You can install NanoStringNorm from CRAN using:

install.packages("NanoStringNorm")

Newer versions of NanoStringNorm (at least from v1.1.21 onwards), depend on the vsn Bioconductor R package. As NanoStringNorm is not part of Bioconductor, you will need to install this dependency yourself:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("vsn")

Overview

To see the full list of exported functions:

library("CHL26predictor")
ls("package:CHL26predictor")

A quick overview of some of the key functions:

• convert_RCC_to_mat: Converts the RCC files in a directory into a matrix.
• get_normalizer: Returns the normalizer values for each sample.

An introduction vignette has been written to describe how to use the R package.