htgmM

generate FDR matrix of id versus cat

Two papers published in the early 2000's (Zeeberg, B.R., Feng, W., Wang, G. et al.
(2003) <doi:10.1186/gb-2003-4-4-r28>) and (Zeeberg, B.R., Qin, H., Narashimhan, S., et al. (2005)
<doi:10.1186/1471-2105-6-168>) implement 'GoMiner' and 'High Throughput GoMiner'
('HTGM') to map lists of genes to the Gene Ontology (GO) <https://geneontology.org>. Until recently,
these were hosted on a server at The National Cancer Institute (NCI). In order to continue
providing these services to the bio-medical community, I have developed stand-alone versions.
The current package 'HTGM' builds upon my recent package 'GoMiner'.
The output of 'GoMiner' is a heatmap showing the relationship of a single list
of genes and the significant categories into which they map. 'High Throughput GoMiner'
('HTGM') integrates the results of the individual 'GoMiner' analyses. The output of 'HTGM'
is a heatmap showing the relationship of the significant categories derived from each gene list.
The heatmap has only 2 axes, so the identity of the genes are unfortunately
"integrated out of the equation." Because the graphic for the heatmap is implemented
in Scalable Vector Graphics (SVG) technology, it is relatively easy to hyperlink each
picture element to the relevant list of genes. By clicking on the desired picture
element, the user can recover the "lost" genes.

Barry Zeeberg

HTGM

High Throughput 'GoMiner'

htgmM function

<dl><dt>l</dt>
<dd>list of return values of GoMiner()</dd>
<dt>fdrThresh</dt>
<dd>numerical acceptance threshold for fdr</dd></dl>

Arguments

htgmM — htgmM

<dl>

<dt>l</dt>
<dd>list of return values of GoMiner()</dd>


<dt>fdrThresh</dt>
<dd>numerical acceptance threshold for fdr</dd>

</dl>

htgmM: htgmM

Description

Usage

Value

Arguments

Examples