SWATH2stats

Package: SWATH2stats
Type: Package
Title: Transform and Filter SWATH Data for Statistical Packages
Version: 1.2.3
Date: 2016-05-23
Author: Peter Blattmann, Moritz Heusel and Ruedi Aebersold
Maintainer: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Description: This package is intended to transform SWATH data from the
OpenSWATH software into a format readable by other statistics
packages while performing filtering, annotation and FDR
estimation.
License: GPL-3
Depends: R (>= 2.10.0)
Imports: data.table, reshape2, grid, ggplot2, stats
Suggests: testthat, MSstats, aLFQ, knitr
Enhances: imsbInfer
biocViews: Proteomics, Annotation, ExperimentalDesign, Preprocessing,
MassSpectrometry
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2016-05-24 05:50:58 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SWATH2stats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SWATH2stats'
    finding HTML links ... done
    OpenSWATH_data                          html  
    SWATH2stats-package                     html  
Rd warning: /tmp/Rtmp0D7CY2/R.INSTALL71964e93766d/SWATH2stats/man/SWATH2stats-package.Rd:39: missing file link 'aLFQ'
Rd warning: /tmp/Rtmp0D7CY2/R.INSTALL71964e93766d/SWATH2stats/man/SWATH2stats-package.Rd:40: missing file link 'MSstats'
    Spyogenes                               html  
    Study_design                            html  
    assess_decoy_rate                       html  
    assess_fdr_byrun                        html  
    assess_fdr_overall                      html  
    convert4MSstats                         html  
    convert4aLFQ                            html  
    convert4mapDIA                          html  
    convert4pythonscript                    html  
    count_analytes                          html  
    disaggregate                            html  
    filter_all_peptides                     html  
    filter_mscore_all                       html  
    filter_mscore_fdr                       html  
    filter_on_max_peptides                  html  
    filter_on_min_peptides                  html  
    filter_proteotypic_peptides             html  
    import_data                             html  
    mscore4assayfdr                         html  
    mscore4pepfdr                           html  
    mscore4protfdr                          html  
    plot.fdr_cube                           html  
    plot.fdr_table                          html  
    plot_correlation_between_samples        html  
    plot_variation                          html  
    plot_variation_vs_total                 html  
    reduce_OpenSWATH_output                 html  
    sample_annotation                       html  
    transform_MSstats_OpenSWATH             html  
    write_matrix_peptides                   html  
    write_matrix_proteins                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SWATH2stats)
Making 'packages.html' ... done