pathifier-package {pathifier} | R Documentation

## Quantify deregulation of pathways in cancer

### Description

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

### Details

Package: | pathifier
Type: | Package
Version: | 1.0
Date: | 2013-03-15
License: | Artistic-1.0

### Author(s)

Yotam Drier <drier.yotam@mgh.harvard.edu> Maintainer: Assif Yitzhaky <assif.yitzhaky@weizmann.ac.il>

### References

Drier Y, Sheffer M, Domany E. Pathway-based personalized analysis of cancer. Proceedings of the National Academy of Sciences, 2013, vol. 110(16) pp:6388-6393. (www.pnas.org/cgi/doi/10.1073/pnas.1219651110)

See more information on : http://www.weizmann.ac.il/pathifier/

### Examples

    data(KEGG) # Two pathways of the KEGG database
    data(Sheffer) # The colorectal data of Sheffer et al.
    PDS<-quantify_pathways_deregulation(sheffer$data, sheffer$allgenes,
      kegg$gs, kegg$pathwaynames, sheffer$normals, attempts = 100,
      logfile="sheffer.kegg.log", min_exp=sheffer$minexp, min_std=sheffer$minstd)

[Package pathifier version 1.20.0 Index]