SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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.

Author
Peter Blattmann, Moritz Heusel and Ruedi Aebersold
Date of publication
None
Maintainer
Peter Blattmann <blattmann@imsb.biol.ethz.ch>
License
GPL-3
Version
1.4.1

View on Bioconductor

Man pages

assess_decoy_rate
assess_decoy_rate: Assess decoy rate
assess_fdr_byrun
Assess assay, peptide and protein level FDR by run (for each...
assess_fdr_overall
Assess overall FDR in annotated OpenSWATH/pyProphet output...
convert4aLFQ
convert4aLFQ: Convert table into the format for aLFQ
convert4mapDIA
convert4mapDIA: Convert table into the format for mapDIA
convert4MSstats
convert4MSstats: Convert table into the format for MSstats
convert4pythonscript
convert4bashscript: Convert data into the format for running...
count_analytes
count_analytes: Counts analytes in different injections
disaggregate
disaggregate: Transforms the SWATH data from a peptide- to a...
filter_all_peptides
Select all proteins that are supported by peptides.
filter_mscore_all
filter_mscore: Filter openSWATH output table according to...
filter_mscore_fdr
Filter annotated OpenSWATH/pyProphet output table to achieve...
filter_on_max_peptides
Filter only for the highest intense peptides
filter_on_min_peptides
Filter openSWATH output for proteins that are identified by a...
filter_proteotypic_peptides
Filter for proteins that are supported by proteotypic...
import_data
import_data: Transforms the column names from a data frame to...
mscore4assayfdr
Find m_score cutoff to reach a desired FDR on assay level...
mscore4pepfdr
Find m_score cutoff to reach a desired FDR on peptide level...
mscore4protfdr
Find m_score cutoff to reach a desired FDR on protein level...
MSstats_data
Testing dataset in MSstats format
OpenSWATH_data
Testing dataset from OpenSWATH
plot_correlation_between_samples
Plots the correlation between injections.
plot.fdr_cube
Plot functionality for FDR assessment result arrays as...
plot.fdr_table
Plot functionality for results of class "fdr_table" as...
plot_variation
Plots the coefficient of variation for different replicates
plot_variation_vs_total
Plots the total variation versus variation within replicates
reduce_OpenSWATH_output
Reduce columns of OpenSWATH data
sample_annotation
sample_annotation: Annotate the SWATH data with the sample...
Spyogenes
S.pyogenes example data
Study_design
Study design table
SWATH2stats-package
SWATH2stats
transform_MSstats_OpenSWATH
transform_MSstats_OpenSWATH: Transforms column names to...
write_matrix_peptides
write_matrix_peptides: Writes out an overview matrix of...
write_matrix_proteins
write_matrix_proteins: Writes out an overview matrix of...

Files in this package

SWATH2stats/DESCRIPTION
SWATH2stats/NAMESPACE
SWATH2stats/NEWS
SWATH2stats/R
SWATH2stats/R/assess_decoy_rate.R
SWATH2stats/R/assess_fdr_byrun.R
SWATH2stats/R/assess_fdr_overall.R
SWATH2stats/R/convert4MSstats.R
SWATH2stats/R/convert4aLFQ.R
SWATH2stats/R/convert4mapDIA.R
SWATH2stats/R/convert4pythonscript.R
SWATH2stats/R/count_analytes.R
SWATH2stats/R/disaggregate.R
SWATH2stats/R/filter_all_peptides.R
SWATH2stats/R/filter_mscore.R
SWATH2stats/R/filter_mscore_condition.R
SWATH2stats/R/filter_mscore_fdr.R
SWATH2stats/R/filter_mscore_freqobs.R
SWATH2stats/R/filter_on_max_peptides.R
SWATH2stats/R/filter_on_min_peptides.R
SWATH2stats/R/filter_proteotypic_peptides.R
SWATH2stats/R/import_data.R
SWATH2stats/R/mscore4assayfdr.R
SWATH2stats/R/mscore4pepfdr.R
SWATH2stats/R/mscore4protfdr.R
SWATH2stats/R/plot.fdr_cube.R
SWATH2stats/R/plot.fdr_table.R
SWATH2stats/R/plot_correlation_between_samples.R
SWATH2stats/R/plot_variation.R
SWATH2stats/R/plot_variation_vs_total.R
SWATH2stats/R/reduce_OpenSWATH_output.R
SWATH2stats/R/sample_annotation.R
SWATH2stats/R/transform_MSstats_OpenSWATH.R
SWATH2stats/R/write_matrix_peptides.R
SWATH2stats/R/write_matrix_proteins.R
SWATH2stats/build
SWATH2stats/build/vignette.rds
SWATH2stats/data
SWATH2stats/data/MSstats_data.txt.gz
SWATH2stats/data/OpenSWATH_data.txt.gz
SWATH2stats/data/Spyogenes.rda
SWATH2stats/data/Study_design.txt.gz
SWATH2stats/data/datalist
SWATH2stats/inst
SWATH2stats/inst/CITATION
SWATH2stats/inst/doc
SWATH2stats/inst/doc/SWATH2stats_example_script.R
SWATH2stats/inst/doc/SWATH2stats_example_script.Rmd
SWATH2stats/inst/doc/SWATH2stats_example_script.pdf
SWATH2stats/inst/doc/SWATH2stats_vignette.R
SWATH2stats/inst/doc/SWATH2stats_vignette.Rnw
SWATH2stats/inst/doc/SWATH2stats_vignette.pdf
SWATH2stats/man
SWATH2stats/man/MSstats_data.Rd
SWATH2stats/man/OpenSWATH_data.Rd
SWATH2stats/man/SWATH2stats-package.Rd
SWATH2stats/man/Spyogenes.Rd
SWATH2stats/man/Study_design.Rd
SWATH2stats/man/assess_decoy_rate.Rd
SWATH2stats/man/assess_fdr_byrun.Rd
SWATH2stats/man/assess_fdr_overall.Rd
SWATH2stats/man/convert4MSstats.Rd
SWATH2stats/man/convert4aLFQ.Rd
SWATH2stats/man/convert4mapDIA.Rd
SWATH2stats/man/convert4pythonscript.Rd
SWATH2stats/man/count_analytes.Rd
SWATH2stats/man/disaggregate.Rd
SWATH2stats/man/filter_all_peptides.Rd
SWATH2stats/man/filter_mscore_all.Rd
SWATH2stats/man/filter_mscore_fdr.Rd
SWATH2stats/man/filter_on_max_peptides.Rd
SWATH2stats/man/filter_on_min_peptides.Rd
SWATH2stats/man/filter_proteotypic_peptides.Rd
SWATH2stats/man/import_data.Rd
SWATH2stats/man/mscore4assayfdr.Rd
SWATH2stats/man/mscore4pepfdr.Rd
SWATH2stats/man/mscore4protfdr.Rd
SWATH2stats/man/plot.fdr_cube.Rd
SWATH2stats/man/plot.fdr_table.Rd
SWATH2stats/man/plot_correlation_between_samples.Rd
SWATH2stats/man/plot_variation.Rd
SWATH2stats/man/plot_variation_vs_total.Rd
SWATH2stats/man/reduce_OpenSWATH_output.Rd
SWATH2stats/man/sample_annotation.Rd
SWATH2stats/man/transform_MSstats_OpenSWATH.Rd
SWATH2stats/man/write_matrix_peptides.Rd
SWATH2stats/man/write_matrix_proteins.Rd
SWATH2stats/scripts
SWATH2stats/scripts/featurealigner2msstats_withRT.py
SWATH2stats/tests
SWATH2stats/tests/test-all.R
SWATH2stats/tests/testthat
SWATH2stats/tests/testthat/test_FDRfunctions.R
SWATH2stats/tests/testthat/test_convert.R
SWATH2stats/tests/testthat/test_filtering.R
SWATH2stats/tests/testthat/test_loading.R
SWATH2stats/tests/testthat/test_matrixwriting.R
SWATH2stats/tests/testthat/test_plots.R
SWATH2stats/vignettes
SWATH2stats/vignettes/SWATH2stats_example_script.Rmd
SWATH2stats/vignettes/SWATH2stats_vignette.Rnw