as.data.frame.GCalign

Based on an object of class "GCalign" that was created using <code>align_chromatograms</code>, a list of data frames for each variable in the dataset is returned. Within data frames rows represent substances and columns are variables (i.e. substances).

Aligns peak based on peak retention times and matches homologous peaks
across samples. The underlying alignment procedure comprises three sequential steps.
(1) Full alignment of samples by linear transformation of retention times to
maximise similarity among homologous peaks (2) Partial alignment of peaks within
a user-defined retention time window to cluster homologous peaks (3) Merging rows
that are likely representing homologous substances (i.e. no sample shows peaks in
both rows and the rows have similar retention time means). The algorithm is described in detail
in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.

Meinolf Ottensmann

GCalignR

Simple Peak Alignment for Gas-Chromatography Data

Martin Stoffel

Hazel J. Nichols

Joseph I. Hoffman

as.data.frame.GCalign function

<dl><dt>x</dt>
<dd>An object of class "GCalign". See <code>align_chromatograms</code> for details.</dd>
<dt>row.names</dt>
<dd><code>NULL</code> or a character vector giving the row
 names for the data frame. Missing values are not allowed.</dd>
<dt>optional</dt>
<dd>logical. If <code>TRUE</code>, setting row names and
 converting column names (to syntactic names: see
 <code><a href="/link/make.names?package=GCalignR&version=1.0.7" data-mini-rdoc="GCalignR::make.names">make.names</a></code>) is optional. Note that all of R's
 base package <code><a href="/link/as.data.frame()?package=GCalignR&version=1.0.7" data-mini-rdoc="GCalignR::as.data.frame()">as.data.frame()</a></code> methods use
 <code>optional</code> only for column names treatment, basically with the
 meaning of <code><a href="/link/data.frame?package=GCalignR&version=1.0.7" data-mini-rdoc="GCalignR::data.frame">data.frame</a>(*, check.names = !optional)</code>.
 See also the <code>make.names</code> argument of the <code>matrix</code> method.</dd>
<dt>...</dt>
<dd>additional arguments to be passed to or from methods.</dd></dl>

Arguments

Meinolf Ottensmann (meinolf.ottensmann@web.de) &amp; Martin Stoffel (martin.adam.stoffel@gmail.com)

Author

Output aligned data in form of a data frame for each variable — as.data.frame.GCalign

<dl>

<dt>x</dt>
<dd>An object of class "GCalign". See <code>align_chromatograms</code> for details.</dd>


<dt>row.names</dt>
<dd><code>NULL</code> or a character vector giving the row
 names for the data frame. Missing values are not allowed.</dd>


<dt>optional</dt>
<dd>logical. If <code>TRUE</code>, setting row names and
 converting column names (to syntactic names: see
 <code><a href='https://rdrr.io/r/base/make.names.html'>make.names</a></code>) is optional. Note that all of R's
 base package <code><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame()</a></code> methods use
 <code>optional</code> only for column names treatment, basically with the
 meaning of <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>(*, check.names = !optional)</code>.
 See also the <code>make.names</code> argument of the <code>matrix</code> method.</dd>


<dt>...</dt>
<dd>additional arguments to be passed to or from methods.</dd>

</dl>

as.data.frame.GCalign: Output aligned data in form of a data frame for each variable

Description

Usage

Arguments

Author

Examples