grabMzmlMS1

Extract the MS1 data from an mzML nodeset

R-based access to mass-spectrometry (MS) data. While many packages
exist to process MS data, many of these make it difficult to
access the underlying mass-to-charge ratio (m/z), intensity, and
retention time of the files
themselves. This package is designed to format MS data in a tidy fashion and
allows the user perform the plotting and analysis.

William Kumler

RaMS

R Access to Mass-Spec Data

Ricardo Cunha

Ethan Bass

grabMzmlMS1 function

<dl><dt>xml_data</dt>
<dd>An `xml2` nodeset, usually created by applying `read_xml` to
an mzML file.</dd>
<dt>rtrange</dt>
<dd>A vector of length 2 containing an upper and lower bound on
retention times of interest. Providing a range here can speed up load times
(although not enormously, as the entire file must still be read) and reduce
the final object's size.</dd>
<dt>file_metadata</dt>
<dd>Information about the file used to decode the binary
arrays containing m/z and intensity information.</dd>
<dt>prefilter</dt>
<dd>The lowest intensity value of interest, used to reduce file
size (and especially useful for profile mode data with many 0 values)</dd>
<dt>incl_polarity</dt>
<dd>Boolean determining whether the polarity of the scan
should be returned as a column in the table (positive mode = 1, negative
mode = -1)</dd></dl>

Arguments

Extract the MS1 data from an mzML nodeset — grabMzmlMS1

<dl>

<dt>xml_data</dt>
<dd>An `xml2` nodeset, usually created by applying `read_xml` to
an mzML file.</dd>


<dt>rtrange</dt>
<dd>A vector of length 2 containing an upper and lower bound on
retention times of interest. Providing a range here can speed up load times
(although not enormously, as the entire file must still be read) and reduce
the final object's size.</dd>


<dt>file_metadata</dt>
<dd>Information about the file used to decode the binary
arrays containing m/z and intensity information.</dd>


<dt>prefilter</dt>
<dd>The lowest intensity value of interest, used to reduce file
size (and especially useful for profile mode data with many 0 values)</dd>


<dt>incl_polarity</dt>
<dd>Boolean determining whether the polarity of the scan
should be returned as a column in the table (positive mode = 1, negative
mode = -1)</dd>

</dl>

grabMzmlMS1: Extract the MS1 data from an mzML nodeset

Description

Usage

Value

Arguments