Sheffer

datasets

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.

Assif Yitzhaky

pathifier

Quantify deregulation of pathways in cancer

Sheffer function

<dl>
    <dt><code>data</code></dt><dd>the expression data</dd> <dt><code>samples</code></dt><dd>sample names</dd> <dt><code>normals</code></dt><dd>which of the samples is a normal sample</dd> <dt><code>minstd</code></dt><dd>minimal standart deviation allowed</dd> <dt><code>minexp</code></dt><dd>minimal value of experssion allowed</dd> <dt><code>allgenes</code></dt><dd>the list of genes (by official gene symbol)</dd> </dl> 

Format

Sheffer et.\ al. Association of survival and disease progression with chromosomal instability: A genomic exploration of colorectal cancer.
<em>PNAS</em>, 2009, Vol 106(17) pp: 7131-7136.

Sheffer: Sheffer et al. colorectal dataset

Description

Usage

Arguments

Format

Source

Examples