processDataMutSurv

This functions finds matched individuals in <code>data.mut</code> and <code>data.surv</code>, and outputs the two data sets with only matched individuals.

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

processDataMutSurv function

<dl> <dt>data.mut</dt>
<dd>Integer matrix of genes by cases. The first column contains gene names. Each of the other columns contains mutation patterns of a case: 0 as wildtype, 1 amplification and -1 deletion.</dd> <dt>data.surv</dt>
<dd>Data frame containing case ID, survival time and survival status. Cases do not need to match those in <code>data.mut</code>.</dd> <dt>colTime</dt>
<dd>Scalar indicating which column in <code>data.surv</code> contains the survival time.</dd> <dt>colStatus</dt>
<dd>A character string indicating which column in <code>data.surv</code> contains the survival status: "DECEASED" or "LIVING".</dd></dl>

Arguments

Author

Find matched individuals in mutation and survival data — processDataMutSurv

<dl>

 <dt>data.mut</dt>
<dd>Integer matrix of genes by cases. The first column contains gene names. Each of the other columns contains mutation patterns of a case: 0 as wildtype, 1 amplification and -1 deletion.</dd>

 <dt>data.surv</dt>
<dd>Data frame containing case ID, survival time and survival status. Cases do not need to match those in <code>data.mut</code>.</dd>

 <dt>colTime</dt>
<dd>Scalar indicating which column in <code>data.surv</code> contains the survival time.</dd>

 <dt>colStatus</dt>
<dd>A character string indicating which column in <code>data.surv</code> contains the survival status: "DECEASED" or "LIVING".</dd>

</dl>

processDataMutSurv: Find matched individuals in mutation and survival data

Description

Usage

Value

Arguments

Author

References

See Also