calculateRC

This function calculates Random Control (RC)

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

calculateRC function

<dl><dt>df</dt>
<dd>a data frame containng p-values</dd>
<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>TF.col</dt>
<dd>the name of the column that contains the TF names</dd>
<dt>lambda</dt>
<dd>a user-specified threshold of E-value (default: 0.05)</dd>
<dt>nRep</dt>
<dd>number of random selections (default: 100)</dd></dl>

Arguments

Atsushi Fukushima
Definition:
m is the number of target genes annotated for the TF
under consideration
n is the number of query genes
N is the number of regulations in the catalog
k is the number of query genes that are annotated as
regulated by TF (i.e., the intersection between the
query and the TF signature)

Author

calculates Random Control (RC) — calculateRC

<dl>

<dt>df</dt>
<dd>a data frame containng p-values</dd>


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


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


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

</dl>

calculateRC: calculates Random Control (RC)

Description

Usage

Value

Arguments

Author

References

Examples