read.bibliospec {specL} | R Documentation

## BiblioSpec Reader

### 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

[Package specL version 1.20.0 Index]