calculateTFactS

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

calculateTFactS 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>TFs</dt>
<dd>a character vector of transcription factor</dd>
<dt>all.targets</dt>
<dd>a character vector of all target genes</dd>
<dt>Q.value</dt>
<dd>logical. If it is TRUE, Q.value by Storey method.</dd>
<dt>lambda1</dt>
<dd>a vector of the lambda values utilized to obtain pi0.lambda</dd>
<dt>lambda2</dt>
<dd>a user-specified threshold of E-value (default: 0.05)</dd>
<dt>nRep</dt>
<dd>number of random selections (default: 100)</dd>
<dt>TF.col</dt>
<dd>the name of the column that contains the TF names</dd></dl>

Arguments

Author

calculates TFactS — calculateTFactS

<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>TFs</dt>
<dd>a character vector of transcription factor</dd>


<dt>all.targets</dt>
<dd>a character vector of all target genes</dd>


<dt>Q.value</dt>
<dd>logical. If it is TRUE, Q.value by Storey method.</dd>


<dt>lambda1</dt>
<dd>a vector of the lambda values utilized to obtain pi0.lambda</dd>


<dt>lambda2</dt>
<dd>a user-specified threshold of E-value (default: 0.05)</dd>


<dt>nRep</dt>
<dd>number of random selections (default: 100)</dd>


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

</dl>

calculateTFactS: calculates TFactS

Description

Usage

Value

Arguments

Author

References

Examples