write.gmt

This function write a file containing the Metabolite Set informtation in the format GMT defined by GenePattern.

A new pipeline to explore chemical structural similarity across metabolites. It allows the metabolite classification in structurally-related modules and identifies common shared functional groups. The KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705>, Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>, and Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. (2023) Bioinformatics Advances <doi:10.1093/bioadv/vbad053>.

Stefano Cacciatore

MetChem

Chemical Structural Similarity Analysis

Ebtesam Abdel-Shafy

Tadele Melak

David A. MacIntyre

Giorgia Zadra

Luiz F. Zerbini

Silvano Piazza

write.gmt function

<dl> <dt>sub</dt>
<dd>A matrix.</dd> <dt>address</dt>
<dd>The address of the file should be saved.</dd> <dt>min_entry</dt>
<dd>The minimum number of metabolites for each metabolite set.</dd> <dt>max_entry</dt>
<dd>The maximum number of metabolites for each metabolite set.</dd></dl>

Arguments

Write a GMT file — write.gmt

<dl>

 <dt>sub</dt>
<dd>A matrix.</dd>

 <dt>address</dt>
<dd>The address of the file should be saved.</dd>

 <dt>min_entry</dt>
<dd>The minimum number of metabolites for each metabolite set.</dd>

 <dt>max_entry</dt>
<dd>The maximum number of metabolites for each metabolite set.</dd>

</dl>

write.gmt: Write a GMT file

Description

Usage

Value

Arguments

See Also