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This functions transforms the column names from a data frame from another format to a data frame with column names used by the OpenSWATH output and required for these functions. During executing of the function the corresponding columns for each column in the data need to be selected. For columns that do not corresond to a certain column 'not applicable' needs to be selected and the column names are not changed.
● Data Source:
BioConductor
● Keywords:
● Alias: import_data
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This function estimates the m_score cutoff required in a dataset to reach a given overall assay level FDR. It counts target and decoy assays at high resolution across the m_score cutoffs and reports a useful m_score cutoff - assay FDR pair close to the supplied fdr_target level over the entire dataset. The m_score cutoff is returned by the function and can be used in the context of the filtering functions, e.g.:
● Data Source:
BioConductor
● Keywords:
● Alias: mscore4assayfdr
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This function estimates the m_score cutoff required in a dataset to reach a given overall peptide level FDR. It counts target and decoy peptides (unique FullPeptideName) at high resolution across the m_score cutoffs and reports a useful m_score cutoff - peptide FDR pair close to the supplied fdr_target level over the entire dataset. The m_score cutoff is returned by the function and can be used in the context of the filtering functions, e.g.:
● Data Source:
BioConductor
● Keywords:
● Alias: mscore4pepfdr
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This function estimates the m_score cutoff required in a dataset to reach a given overall protein level FDR. This filter is to be used with caution as the resulting quantitative matrix is relatively sparse. It can be filled with quantitative values at a lower FDR quality level. It counts target and decoy peptides (unique ProteinName) at high resolution across the m_score cutoffs and reports a useful m_score cutoff - peptide FDR pair close to the supplied fdr_target level over the entire dataset. The m_score cutoff is returned by the function and can be used in the context of the filtering functions, e.g.:
● Data Source:
BioConductor
● Keywords:
● Alias: mscore4protfdr
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This function creates standard plots from result arrays as produced by e.g. the function assess_fdr_byrun(), visualizig assay, peptide and protein level FDR for each run at m-score cutoffs 1e-2 and 1e-3. Furthermore, Target and Decoy ID numbers are visualized.
● Data Source:
BioConductor
● Keywords:
● Alias: plot.fdr_cube
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This function created standard plots from results of class "fdr_table" as produced by e.g. the function assess_fdr_overall() visualizig ID numbers in dependence of estimated FDR and also estimated FDR in dependence of m_score cutoff.
● Data Source:
BioConductor
● Keywords:
● Alias: plot.fdr_table
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This function plots the Pearson's and Spearman correlation between samples. If decoys are present these are removed before plotting.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_correlation_between_samples
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This function plots the coefficient of variation within replicates for a given value. If decoys are present these are removed before plotting.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_variation
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This function plots the total variation and the variation within replicates for a given value. If decoys are present these are removed before plotting.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_variation_vs_total
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This function selects the columns from the standard OpenSWATH output to column needed for MSstats, aLFQ and mapDIA.
● Data Source:
BioConductor
● Keywords:
● Alias: reduce_OpenSWATH_output
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