isobar-reports: Isobar reports
In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description Usage Arguments Details Author(s) See Also

Generation of LaTeX and XLS reports is helped with functions which facilitate the gathering of relevant information and creation of tikz plots. create.reports parses properties (by calling load.properties) and initialize environments and computations (by calling initialize.env) required by the reports, calls Sweave and pdflatex.

create.reports(properties.file = "properties.R", 
               global.properties.file = system.file("report","properties.R", package = "isobar"),
               args = NULL, ...,
               recreate.properties.env = TRUE, recreate.report.env = TRUE)

load.properties(properties.file = "properties.R",
                global.properties.file = system.file("report","properties.R",package="isobar"),
                args = NULL, ...)

initialize.env(env, properties.env)

`properties.file`	File which holds the parameters for data analysis and report generation. It is parsed as R code after the global report configuration file `global.properties.file` and defines peaklists, identification files, significance levels, etc. See the global properties file for the available options and values.
`global.properties.file`	`system.file("report","properties.R",package="isobar")`
`args`	Additional (command line) arguments which overrids those in `properties.file`.
`...`	Additional properties.
`recreate.properties.env`	Whether a properties.env existing in the global environment should be used, or it should be recreated.
`recreate.report.env`	Whether a report.env existing in the global environment should be used, or it should be recreated.
`env`	Item to be initialized.
`properties.env`	Environment into which properties are read.

The directory inst in the isobar installation directory system.file("inst",package="isobar") contains R, Sweave, and LaTeX files as examples of how to create XLS and PDF reports using isobar.

create_reports.R

Call with Rscript. It is the main file which

parses command line options. --compile and --zip are parsed directly and given as arguments to create.reports. Other arguments are given load.properties.
calls a perl script to generate a XLS report
generates a LaTeX quality control and analysis report

for the XLS report the script pl/tab2xls.pl is used, which concetenates CSV files to a XLS. See Perl requirements. Sweave is called on report/isobar-qc.Rnw and report/isobar-analysis.Rnw. All files are written the working directory.

isobar-qc.Rnw