protti: qc_missed_cleavages – R documentation

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qc_missed_cleavages

Check missed cleavages

Description

Calculates the percentage of missed cleavages for each sample (by count or intensity).The default settings remove grouping variables without quantitative information (intensity is NA). These will not be used for the calculation of missed cleavage percentages.

Usage

qc_missed_cleavages(
  data,
  sample,
  grouping,
  missed_cleavages,
  intensity,
  remove_na_intensities = TRUE,
  method = "count",
  plot = FALSE,
  interactive = FALSE
)

Arguments

`data`	A data frame containing at least sample names, peptide or precursor identifiers and missed cleavage counts for each peptide or precursor.
`sample`	the name of the column in the data data frame containing the sample name.
`grouping`	the name of the column in the data data frame containing either precursor or peptide identifiers.
`missed_cleavages`	the name of the column in the data data frame containing the counts of missed cleavages per peptide or precursor.
`intensity`	the name of the column containing the corresponding raw or normalised intensity values (not log2) for each peptide or precursor. Required when "intensity" is chosen as the method.
`remove_na_intensities`	Logical specifying if sample/grouping combinations with intensities that are NA (not quantified IDs) should be dropped from the data frame for analysis of missed cleavages. Default is TRUE since we are usually interested in quantifiable peptides. This is only relevant for method = "count".
`method`	character vector indicating the method used for evaluation. "count" calculates the percentage of missed cleavages based on counts of the corresponding peptide or precursor, "intensity" calculates the percentage of missed cleavages by intensity of the corresponding peptide or precursor.
`plot`	A logical indicating whether the result should be plotted.
`interactive`	Argument specifying whether the plot should be interactive (default is FALSE).

Value

A data frame that contains the calculated percentage made up by the sum of all peptides or precursors containing the corresponding amount of missed cleavages.

Examples

## Not run: 
qc_missed_cleavages(
  data,
  sample = r_file_name,
  grouping = pep_stripped_sequence,
  missed_cleavages = pep_nr_of_missed_cleavages,
  intensity = fg_quantity,
  method = "intensity",
  plot = TRUE
)

## End(Not run)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release