README.md

In yeswzc/cnsTumorMNN: cnsTumorMNN package

cnsTumorMNN

• Query nearest neighbors in 'Capper et al.. Nature. 2018' for central nervous tumors. Meanwhile, a KNN classification with calibrated score, umap, tsne will also be plotted.

• R/3.6 is suggested.

• (The package is not been well tested yet.)

How to install

• There are many packages required before installations. The packages include but not limitted to umap, Rtsne, minfi, LUMP, RFpurify, dplyr, caret, glmnet, plotly, RANN, knitr, kableExtra, RColorBrewer...

• Install LUMP

  devtools::install_github("yeswzc/LUMP")

• Install cnsTumorMNN, an imperfect package

  Download the package from here: https://github.com/yeswzc/cnsTumorMNN/releases and then

install.packages("cnsTumorMNN_0.1.0.tar.gz", repos = NULL, type = "source")

devtools::install_github("yeswzc/cnsTumorMNN") #This may not work.

How to Run the code

After install finished. Download 'pipeline.v5.R' and 'Generate_HTMLreport.v5.Rmd', then you can run Rscript /path/to/pipeline.v5.R /path/to/idat_directory/ output_prefix

Sample_Sheet.csv is required in the idat_directory.

Reference:

Wu et al.. Impact of the methylation classifier and ancillary methods on CNS tumor diagnostics. Neuro-oncology, 2021 (https://doi.org/10.1093/neuonc/noab227). Capper et al.. DNA methylation-based classification of central nervous system tumours. Nature, 2018. (DOI: 10.1038/nature26000)

yeswzc/cnsTumorMNN documentation built on May 23, 2024, 12:03 p.m.