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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SWATH2stats")
AuthorPeter Blattmann, Moritz Heusel and Ruedi Aebersold
Bioconductor views Annotation ExperimentalDesign MassSpectrometry Preprocessing Proteomics
Date of publicationNone
MaintainerPeter Blattmann <blattmann@imsb.biol.ethz.ch>
LicenseGPL-3
Version1.4.1

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...

Functions

assess_decoy_rate Man page
assess_fdr_byrun Man page
assess_fdr_overall Man page
convert4aLFQ Man page
convert4mapDIA Man page
convert4MSstats Man page
convert4pythonscript Man page
count_analytes Man page
disaggregate Man page
filter_all_peptides Man page
filter_mscore Man page
filter_mscore_condition Man page
filter_mscore_fdr Man page
filter_mscore_freqobs Man page
filter_on_max_peptides Man page
filter_on_min_peptides Man page
filter_proteotypic_peptides Man page
import_data Man page
mscore4assayfdr Man page
mscore4pepfdr Man page
mscore4protfdr Man page
MSstats_data Man page
OpenSWATH_data Man page
OpenSWATH_data_FDR Man page
plot_correlation_between_samples Man page
plot.fdr_cube Man page
plot.fdr_table Man page
plot_variation Man page
plot_variation_vs_total Man page
reduce_OpenSWATH_output Man page
sample_annotation Man page
Spyogenes Man page
Study_design Man page
SWATH2stats Man page
SWATH2stats-package Man page
transform_MSstats_OpenSWATH Man page
write_matrix_peptides Man page
write_matrix_proteins Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.