env.plot

Plots the Z statistics at each position within the environment for the requested amino acid.

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

env.plot function

<dl><dt>Z</dt>
<dd>a matrix containing the standardized difference in frequencies (positive - control).</dd>
<dt>aa</dt>
<dd>the amino acid of interest.</dd>
<dt>pValue</dt>
<dd>the p-Value chosen to confer statistical significance.</dd>
<dt>ylim</dt>
<dd>range of the dependent variable. If we pass the argument 'automatic', the function will choose a suitable range for you.</dd>
<dt>ty</dt>
<dd>what type of plot should be drawn ("p": points, "l": lines, "b": both).</dd>
<dt>title</dt>
<dd>character string giving a title for the plot.</dd></dl>

Arguments

Author

Differential Sequence Environment Plot — env.plot

<dl>

<dt>Z</dt>
<dd>a matrix containing the standardized difference in frequencies (positive - control).</dd>


<dt>aa</dt>
<dd>the amino acid of interest.</dd>


<dt>pValue</dt>
<dd>the p-Value chosen to confer statistical significance.</dd>


<dt>ylim</dt>
<dd>range of the dependent variable. If we pass the argument 'automatic', the function will choose a suitable range for you.</dd>


<dt>ty</dt>
<dd>what type of plot should be drawn ("p": points, "l": lines, "b": both).</dd>


<dt>title</dt>
<dd>character string giving a title for the plot.</dd>

</dl>

env.plot: Differential Sequence Environment Plot

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples