Files in SWATH2stats
Transform and Filter SWATH Data for Statistical Packages

README.Rmd README.md
NEWS
NAMESPACE
DESCRIPTION
build/vignette.rds
data/Study_design.txt.gz
data/datalist
data/OpenSWATH_data.txt.gz
data/Spyogenes.rda
data/MSstats_data.txt.gz
R/convert4MSstats.R R/assess_fdr_byrun.R R/mscore4pepfdr.R R/filter_proteotypic_peptides.R R/reduce_OpenSWATH_output.R R/JPP_update.R R/count_analytes.R R/sample_annotation.R R/convert4aLFQ.R R/filter_mscore_freqobs.R R/mscore4assayfdr.R R/filter_on_max_peptides.R R/filter_mscore.R R/assess_fdr_overall.R R/unifyProteinGroupLabels.R R/plot.fdr_cube.R R/write_matrix_proteins.R R/convert4mapDIA.R R/write_matrix_peptides.R R/import_data.R R/transform_MSstats_OpenSWATH.R R/plot.fdr_table.R R/plot_correlation_between_samples.R R/removeDecoyProteins.R R/plot_variation_vs_total.R R/convert4pythonscript.R R/filter_on_min_peptides.R R/convert4PECA.R R/assess_decoy_rate.R R/convert_protein_ids.R R/validate_columns.R R/filter_mscore_fdr.R R/filter_mscore_condition.R R/data.R R/filter_all_peptides.R R/mscore4protfdr.R R/disaggregate.R R/plot_variation.R
vignettes/SWATH2stats_vignette.Rnw
vignettes/SWATH2stats_example_script.Rmd man/add_genesymbol.Rd man/plot_correlation_between_samples.Rd man/filter_on_min_peptides.Rd man/convert4mapDIA.Rd man/assess_fdr_overall.Rd man/convert4aLFQ.Rd man/filter_proteotypic_peptides.Rd man/MSstats_data.Rd man/transform_MSstats_OpenSWATH.Rd man/removeDecoyProteins.Rd man/mscore4pepfdr.Rd man/assess_fdr_byrun.Rd man/write_matrix_proteins.Rd man/convert4MSstats.Rd man/convert4PECA.Rd man/JPP_update.Rd man/reduce_OpenSWATH_output.Rd man/filter_on_max_peptides.Rd man/Study_design.Rd man/plot.fdr_table.Rd man/Spyogenes.Rd man/rmDecoyProt.Rd man/plot_variation_vs_total.Rd man/filter_mscore_condition.Rd man/disaggregate.Rd man/filter_mscore_fdr.Rd man/mscore4assayfdr.Rd man/filter_all_peptides.Rd man/import_data.Rd man/mscore4protfdr.Rd man/assess_decoy_rate.Rd man/count_analytes.Rd man/plot.fdr_cube.Rd man/write_matrix_peptides.Rd man/validate_columns.Rd man/filter_mscore_freqobs.Rd man/plot_variation.Rd man/convert_protein_ids.Rd man/filter_mscore.Rd man/OpenSWATH_data.Rd man/convert4pythonscript.Rd man/load_mart.Rd man/sample_annotation.Rd man/unifyProteinGroupLabels.Rd tests/test-all.R tests/testthat/test_filtering.R tests/testthat/test_loading.R tests/testthat/test_FDRfunctions.R tests/testthat/test_biomart.R tests/testthat/test_matrixwriting.R tests/testthat/test_convert.R tests/testthat/test_plots.R
inst/CITATION
inst/doc/SWATH2stats_example_script.pdf inst/doc/SWATH2stats_vignette.R
inst/doc/SWATH2stats_vignette.Rnw
inst/doc/SWATH2stats_vignette.pdf inst/doc/SWATH2stats_example_script.Rmd inst/doc/SWATH2stats_example_script.R
inst/scripts/featurealigner2msstats_withRT.py
SWATH2stats documentation built on Nov. 8, 2020, 7:47 p.m.