readMet

This function extract metabocards of your metabolites dataset from http://www.hmdb.ca/metabolites/ database and store all of this information in a list.

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

readMet function

<dl> <dt>ID</dt>
<dd>A vector containg the HMDBcodes (i.e., metabolite IDs) of metabolites dataset.</dd> <dt>address</dt>
<dd>Optional address where the MetaboCards are located. The default address is http://www.hmdb.ca/metabolites/.</dd> <dt>remove</dt>
<dd>A logic value. If true, missing and wrong HMDB IDs are removed.</dd></dl>

Arguments

Metabolite Cards Reading — readMet

<dl>

 <dt>ID</dt>
<dd>A vector containg the HMDBcodes (i.e., metabolite IDs) of metabolites dataset.</dd>

 <dt>address</dt>
<dd>Optional address where the MetaboCards are located. The default address is http://www.hmdb.ca/metabolites/.</dd>

 <dt>remove</dt>
<dd>A logic value. If true, missing and wrong HMDB IDs are removed.</dd>

</dl>

readMet: Metabolite Cards Reading

Description

Usage

Value

Arguments

See Also

Examples