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.

AuthorPeter Blattmann, Moritz Heusel and Ruedi Aebersold
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

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

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.