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
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 overall FDR in annotated OpenSWATH/pyProphet output table in dependence of m_score cutoff
Plots the total variation versus variation within replicates
transform_MSstats_OpenSWATH
transform_MSstats_OpenSWATH: Transforms column names to OpenSWATH column names
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
Find m_score cutoff to reach a desired FDR on assay level (over the entire OpenSWATH/pyProphet output table)
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()
convert4bashscript: Convert data into the format for running a bash script
filter_mscore: Filter openSWATH output table according to mscore
Select all proteins that are supported by peptides.
convert4mapDIA: Convert table into the format for mapDIA
Reduce columns of OpenSWATH data
convert4MSstats: Convert table into the format for MSstats
filter_proteotypic_peptides
Filter for proteins that are supported by proteotypic peptides.
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
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 openSWATH output for proteins that are identified by a minimum of n independent peptides
Filter only for the highest intense 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.