read.bibliospec: BiblioSpec Reader

In specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Description

This function reads a BiblioSpec generated file and returns a list of tandem mass specs (psm objects), peptide assignments, retention times, and modifications records. The type of the data structire which is returned is called psmSet.

Usage

    read.bibliospec(file)

Arguments

file	the name of the BiblioSpec generated SQLite file.

Details

The function performs a SQL query on the SQLite files generated by bibliospec using the RSQLite package. The function is required for generating spec libraries used in a SWATH workflow.

BiblioSpec files are generated by using Skyline.

Value

It returns a list which can be read by the genSwathIonLib function and the protViz::peakplot function.

Author(s)

Christian Panse, 2014, 2015

See Also

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

https://skyline.gs.washington.edu/labkey/project/home/software/BiblioSpec/begin.view

http://www.sqlite.org/

?SQLite

Examples

    read.bibliospec

specL documentation built on Nov. 8, 2020, 7:55 p.m.