extractTFTG

This function extracts information about transcription factor (TF) and
target gene (TG) with TFactS Catalogue (v2).

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

extractTFTG function

<dl><dt>DEGs</dt>
<dd>a character vector of DEGs (differentially expressed genes)</dd>
<dt>catalog</dt>
<dd>a data frame of TFactS catalog (ver. 2)</dd>
<dt>TF.col</dt>
<dd>the name of the column that contains the TF names</dd>
<dt>TG.col</dt>
<dd>the name of the column that contains the TG names</dd></dl>

Arguments

Author

extracts transcription factor (TF) and target gene (TG) information — extractTFTG

<dl>

<dt>DEGs</dt>
<dd>a character vector of DEGs (differentially expressed genes)</dd>


<dt>catalog</dt>
<dd>a data frame of TFactS catalog (ver. 2)</dd>


<dt>TF.col</dt>
<dd>the name of the column that contains the TF names</dd>


<dt>TG.col</dt>
<dd>the name of the column that contains the TG names</dd>

</dl>

extractTFTG: extracts transcription factor (TF) and target gene (TG) information

Description

Usage

Value

Arguments

Author

Examples