Man pages for Bioconductor-mirror/SWATH2stats
Transform and Filter SWATH Data for Statistical Packages

assess_decoy_rateassess_decoy_rate: Assess decoy rate
assess_fdr_byrunAssess assay, peptide and protein level FDR by run (for each...
assess_fdr_overallAssess overall FDR in annotated OpenSWATH/pyProphet output...
convert4aLFQconvert4aLFQ: Convert table into the format for aLFQ
convert4mapDIAconvert4mapDIA: Convert table into the format for mapDIA
convert4MSstatsconvert4MSstats: Convert table into the format for MSstats
convert4pythonscriptconvert4bashscript: Convert data into the format for running...
count_analytescount_analytes: Counts analytes in different injections
disaggregatedisaggregate: Transforms the SWATH data from a peptide- to a...
filter_all_peptidesSelect all proteins that are supported by peptides.
filter_mscore_allfilter_mscore: Filter openSWATH output table according to...
filter_mscore_fdrFilter annotated OpenSWATH/pyProphet output table to achieve...
filter_on_max_peptidesFilter only for the highest intense peptides
filter_on_min_peptidesFilter openSWATH output for proteins that are identified by a...
filter_proteotypic_peptidesFilter for proteins that are supported by proteotypic...
import_dataimport_data: Transforms the column names from a data frame to...
mscore4assayfdrFind m_score cutoff to reach a desired FDR on assay level...
mscore4pepfdrFind m_score cutoff to reach a desired FDR on peptide level...
mscore4protfdrFind m_score cutoff to reach a desired FDR on protein level...
MSstats_dataTesting dataset in MSstats format
OpenSWATH_dataTesting dataset from OpenSWATH
plot_correlation_between_samplesPlots the correlation between injections.
plot.fdr_cubePlot functionality for FDR assessment result arrays as...
plot.fdr_tablePlot functionality for results of class "fdr_table" as...
plot_variationPlots the coefficient of variation for different replicates
plot_variation_vs_totalPlots the total variation versus variation within replicates
reduce_OpenSWATH_outputReduce columns of OpenSWATH data
removeDecoyProteinsRemoves decoy proteins from the protein group label
sample_annotationsample_annotation: Annotate the SWATH data with the sample...
SpyogenesS.pyogenes example data
Study_designStudy design table
SWATH2stats-packageSWATH2stats
transform_MSstats_OpenSWATHtransform_MSstats_OpenSWATH: Transforms column names to...
unifyProteinGroupLabelsUnify the protein group labels
write_matrix_peptideswrite_matrix_peptides: Writes out an overview matrix of...
write_matrix_proteinswrite_matrix_proteins: Writes out an overview matrix of...
Bioconductor-mirror/SWATH2stats documentation built on June 1, 2017, 2:17 a.m.