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SWATH2stats (version 1.2.3)

Transform and Filter SWATH Data for Statistical Packages

Description

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.

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Version

Version

1.2.3

License

GPL-3

Maintainer

Peter Blattmann

Last Published

February 15th, 2017

Functions in SWATH2stats (1.2.3)

assess_fdr_byrun

Assess assay, peptide and protein level FDR by run (for each MS_injection separately) in OpenSWATH output table

Testing dataset from OpenSWATH

plot_correlation_between_samples

Plots the correlation between injections.

SWATH2stats-package

convert4aLFQ: Convert table into the format for aLFQ

disaggregate: Transforms the SWATH data from a peptide- to a transition-level table.

S.pyogenes example data

assess_fdr_overall

Assess overall FDR in annotated OpenSWATH/pyProphet output table in dependence of m_score cutoff

plot_variation_vs_total

Plots the total variation versus variation within replicates

transform_MSstats_OpenSWATH

transform_MSstats_OpenSWATH: Transforms column names to OpenSWATH column names

filter_mscore_fdr

Filter annotated OpenSWATH/pyProphet output table to achieve a high FDR quality data matrix with controlled overall protein FDR and quantitative values for all peptides mapping to these high-confidence proteins (up to a desired overall peptide level FDR quality).

Study design table

mscore4assayfdr

Find m_score cutoff to reach a desired FDR on assay level (over the entire OpenSWATH/pyProphet output table)

sample_annotation

sample_annotation: Annotate the SWATH data with the sample information

Find m_score cutoff to reach a desired FDR on peptide level (over the entire OpenSWATH/pyProphet output table)

Find m_score cutoff to reach a desired FDR on protein level (over the entire OpenSWATH/pyProphet output table)

Plot functionality for FDR assessment result arrays as produced by e.g. the function assess_fdr_byrun()

convert4pythonscript

convert4bashscript: Convert data into the format for running a bash script

filter_mscore: Filter openSWATH output table according to mscore

filter_all_peptides

Select all proteins that are supported by peptides.

convert4mapDIA: Convert table into the format for mapDIA

reduce_OpenSWATH_output

Reduce columns of OpenSWATH data

convert4MSstats

convert4MSstats: Convert table into the format for MSstats

filter_proteotypic_peptides

Filter for proteins that are supported by proteotypic peptides.

write_matrix_proteins

write_matrix_proteins: Writes out an overview matrix of summed signals per protein identifier (lines) over run_id(columns).

assess_decoy_rate

assess_decoy_rate: Assess decoy rate

Plots the coefficient of variation for different replicates

count_analytes: Counts analytes in different injections

import_data: Transforms the column names from a data frame to the required format.

Plot functionality for results of class "fdr_table" as produced by e.g. the function assess_fdr_overall()

filter_on_min_peptides

Filter openSWATH output for proteins that are identified by a minimum of n independent peptides

filter_on_max_peptides

Filter only for the highest intense peptides

write_matrix_peptides

write_matrix_peptides: Writes out an overview matrix of peptides mapping to a FDR quality controlled protein master list at controlled global peptide FDR quality.