constructDesignMatrix

This function takes the raw RNAi data as input and generates a design matrix for regression. Specifically written for the format of the data set <code>RNAi</code>, which contains four batches. This R function will use <code>batch3</code> as the baseline.

Functions to perform the following analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying gene pairs of multiple mutation patterns; iii) assessing association between gene pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene interaction network). Data and analyses are described in Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. <doi:10.1038/ncomms5828>.

Audrey Q Fu

cancerGI

Analyses of Cancer Gene Interaction

constructDesignMatrix function

<dl><dt>data</dt>
<dd>Matrix of RNAi measurements; includes columns batch, query_gene and template_gene.</dd><dt>covariates</dt>
<dd>Vector of strings; each string is the name of a covariate.</dd></dl>

Arguments

Generate a design matrix from raw RNAi data. — constructDesignMatrix

<dl>

<dt>data</dt>
<dd>Matrix of RNAi measurements; includes columns batch, query_gene and template_gene.</dd>

<dt>covariates</dt>
<dd>Vector of strings; each string is the name of a covariate.</dd>

</dl>

constructDesignMatrix: Generate a design matrix from raw RNAi data.

Description

Usage

Value

Arguments

Examples