rScudo-package: Signature-based Clustering for Diagnostic Purposes

Description Author(s) See Also Examples

Description

SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two sample is computed using a method similar to GSEA. The graph of samples can the be used to perform community clustering or to perform supervised classification of samples in a testing set.

Author(s)

Matteo Ciciani matteo.ciciani@gmail.com, Thomas Cantore cantorethomas@gmail.com

See Also

scudoTrain, scudoNetwork, scudoClassify

Examples

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# To learn more about rScudo, start with the vignette:
browseVignettes("rScudo")

Matteo-Ciciani/scudo documentation built on May 24, 2020, 5:34 a.m.