read_peak_list

Reads the content of text file that is formatted as described in <code>align_chromatograms</code> and converts it to a list.

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

read_peak_list function

<dl><dt>data</dt>
<dd>A text file containing a peak list. See <code>align_chromatograms</code> for details.</dd>
<dt>sep</dt>
<dd>The field separator character. The default is tab separated (<code>sep = '\t'</code>).
See the "sep" argument in <code><a href="/link/read.table?package=GCalignR&version=1.0.7" data-mini-rdoc="GCalignR::read.table">read.table</a></code> for details.</dd>
<dt>rt_col_name</dt>
<dd>A character giving the name of the column containing the retention times. The decimal separator needs to be a point.</dd>
<dt>check</dt>
<dd>logical</dd></dl>

Arguments

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

Author

Read content of a text file and convert it to a list — read_peak_list

<dl>

<dt>data</dt>
<dd>A text file containing a peak list. See <code>align_chromatograms</code> for details.</dd>


<dt>sep</dt>
<dd>The field separator character. The default is tab separated (<code>sep = '\t'</code>).
See the "sep" argument in <code><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></code> for details.</dd>


<dt>rt_col_name</dt>
<dd>A character giving the name of the column containing the retention times. The decimal separator needs to be a point.</dd>


<dt>check</dt>
<dd>logical</dd>

</dl>

read_peak_list: Read content of a text file and convert it to a list

Description

Usage

Value

Arguments

Author

Examples