formatRC

This function formats the result of Random Control (RC)
with random simulation based on Fisher's exact test

R implementation of 'TFactS' to predict which are the
transcription factors (TFs), regulated in a biological condition based on
lists of differentially expressed genes (DEGs) obtained from transcriptome
experiments. This package is based on the 'TFactS' concept by
Essaghir et al. (2010) <doi:10.1093/nar/gkq149> and expands
it. It allows users to perform 'TFactS'-like enrichment approach. The
package can import and use the original catalogue file from the 'TFactS'
as well as users' defined catalogues of interest that are not supported
by 'TFactS' (e.g., Arabidopsis).

Atsushi Fukushima

TFactSR

Enrichment Approach to Predict Which Transcription Factors are
Regulated

formatRC function

<dl><dt>df</dt>
<dd>a data frame of ET including E-values, FDR-BH, and Q-values</dd>
<dt>list</dt>
<dd>a list of the result of RC (ncol = 2)</dd>
<dt>nRep</dt>
<dd>the number of random selections (negative control)</dd></dl>

Arguments

Author

formats the result of Random Control (RC) — formatRC

<dl>

<dt>df</dt>
<dd>a data frame of ET including E-values, FDR-BH, and Q-values</dd>


<dt>list</dt>
<dd>a list of the result of RC (ncol = 2)</dd>


<dt>nRep</dt>
<dd>the number of random selections (negative control)</dd>

</dl>

formatRC: formats the result of Random Control (RC)

Description

Usage

Value

Arguments

Author

Examples