SWATH2stats-package |
SWATH2stats |
assess_decoy_rate |
assess_decoy_rate: Assess decoy rate |
assess_fdr_byrun |
Assess assay, peptide and protein level FDR by run (for each MS_injection separately) in OpenSWATH output table |
assess_fdr_overall |
Assess overall FDR in annotated OpenSWATH/pyProphet output table in dependence of m_score cutoff |
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 a bash script |
count_analytes |
count_analytes: Counts analytes in different injections |
disaggregate |
disaggregate: Transforms the SWATH data from a peptide- to a transition-level table. |
filter_all_peptides |
Select all proteins that are supported by peptides. |
filter_mscore |
filter_mscore: Filter openSWATH output table according to mscore |
filter_mscore_condition |
filter_mscore: Filter openSWATH output table according to mscore |
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). |
filter_mscore_freqobs |
filter_mscore: Filter openSWATH output table according to mscore |
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 minimum of n independent peptides |
filter_proteotypic_peptides |
Filter for proteins that are supported by proteotypic peptides. |
import_data |
import_data: Transforms the column names from a data frame to the required format. |
mscore4assayfdr |
Find m_score cutoff to reach a desired FDR on assay level (over the entire OpenSWATH/pyProphet output table) |
mscore4pepfdr |
Find m_score cutoff to reach a desired FDR on peptide level (over the entire OpenSWATH/pyProphet output table) |
mscore4protfdr |
Find m_score cutoff to reach a desired FDR on protein level (over the entire OpenSWATH/pyProphet output table) |
MSstats_data |
Testing dataset in MSstats format |
OpenSWATH_data |
Testing dataset from OpenSWATH |
OpenSWATH_data_FDR |
Testing dataset from OpenSWATH |
plot.fdr_cube |
Plot functionality for FDR assessment result arrays as produced by e.g. the function assess_fdr_byrun() |
plot.fdr_table |
Plot functionality for results of class "fdr_table" as produced by e.g. the function assess_fdr_overall() |
plot_correlation_between_samples |
Plots the correlation between injections. |
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 information |
Spyogenes |
S.pyogenes example data |
Study_design |
Study design table |
SWATH2stats |
SWATH2stats |
transform_MSstats_OpenSWATH |
transform_MSstats_OpenSWATH: Transforms column names to OpenSWATH column names |
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. |
write_matrix_proteins |
write_matrix_proteins: Writes out an overview matrix of summed signals per protein identifier (lines) over run_id(columns). |