FSA_plotFSdb2Spectra

The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.

Dinesh Barupal

IDSL.FSA

Fragmentation Spectra Analysis (FSA)

Sadjad Fakouri-Baygi

FSA_plotFSdb2Spectra function

<dl> <dt>path</dt>
<dd>Address of .msp file(s)</dd> <dt>allowedUnlink</dt>
<dd>allowedUnlink</dd> <dt>annexName</dt>
<dd>annexName</dd> <dt>FSdb</dt>
<dd>FSdb</dd> <dt>selectedFSdbIDs</dt>
<dd>selected FSdb IDs. When `NULL`, the entire FSDB blocks are plotted.</dd> <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd> <dt>allowedVerbose</dt>
<dd>c(TRUE, FALSE). A `TRUE` allowedVerbose provides messages about the flow of the function.</dd></dl>

Arguments

plot FSdb to Spectra — FSA_plotFSdb2Spectra

<dl>

 <dt>path</dt>
<dd>Address of .msp file(s)</dd>

 <dt>allowedUnlink</dt>
<dd>allowedUnlink</dd>

 <dt>annexName</dt>
<dd>annexName</dd>

 <dt>FSdb</dt>
<dd>FSdb</dd>

 <dt>selectedFSdbIDs</dt>
<dd>selected FSdb IDs. When `NULL`, the entire FSDB blocks are plotted.</dd>

 <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd>

 <dt>allowedVerbose</dt>
<dd>c(TRUE, FALSE). A `TRUE` allowedVerbose provides messages about the flow of the function.</dd>

</dl>

FSA_plotFSdb2Spectra: plot FSdb to Spectra

Description

Usage

Value

Arguments