hdfisher.go

Carries out an enrichment Fisher's test using a hypothesis driven approach.

Contains utilities for the analysis of post-translational modifications (PTMs) in proteins,
with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download,
filter and analyze data from the sulfoxidation database 'MetOSite', and integrate data from other main PTMs
(other databases). Utilities to search and characterize S-aromatic motifs in proteins are also provided.
In addition, functions to analyze sequence environments around modifiable residues in proteins can be found.
For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable
residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
these differential sequence environments are also implemented. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).

Juan Aledo

Analyses of Protein Post-Translational Modifications

Juan Carlos Aledo

hdfisher.go function

<dl><dt>target</dt>
<dd>either a vector containing the UniProt IDs of the target set or the path to the txt file containing the list of IDs.</dd>
<dt>background</dt>
<dd>a dataframe with two columns (Uniprot ID and GO terms) and as many rows as different proteins there are in the background set.</dd>
<dt>query</dt>
<dd>character string defining the query.</dd>
<dt>analysis</dt>
<dd>a character string indicating whether the desired analysis is the enrichment ('enrichment') or depletion ('depletion').</dd></dl>

Arguments

Author

Hypothesis-Driven Fisher Test — hdfisher.go

<dl>

<dt>target</dt>
<dd>either a vector containing the UniProt IDs of the target set or the path to the txt file containing the list of IDs.</dd>


<dt>background</dt>
<dd>a dataframe with two columns (Uniprot ID and GO terms) and as many rows as different proteins there are in the background set.</dd>


<dt>query</dt>
<dd>character string defining the query.</dd>


<dt>analysis</dt>
<dd>a character string indicating whether the desired analysis is the enrichment ('enrichment') or depletion ('depletion').</dd>

</dl>

hdfisher.go: Hypothesis-Driven Fisher Test

Description

Usage

Value

Arguments

Author

References

See Also

Examples