protti: calculate_protein_abundance – R documentation

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calculate_protein_abundance

Label-free protein quantification

Description

Determines relative protein abundances from ion quantification. Only proteins with at least 3 peptides are considered for quantification.

Usage

calculate_protein_abundance(
  data,
  sample,
  protein_id,
  precursor,
  peptide,
  intensity_log2,
  method = "iq",
  for_plot = FALSE,
  retain_columns = NULL
)

Arguments

`data`	A data frame that contains at least the input variables.
`sample`	The name of the column containing the sample name.
`protein_id`	The name of the column containing the protein accession numbers.
`precursor`	The name of the column containing precursors.
`peptide`	The name of the column containing peptide sequences. This column is needed to filter for proteins with at least 3 unique peptides. This can equate to more than three precursors. The quantification is done on the precursor level.
`intensity_log2`	The name of the column containing log2 transformed precursor intensities.
`method`	A character vector specifying with which method protein quantities should be calculated. Possible options include `"sum"`, which takes the sum of all precursor intensities as the protein abundance. Another option is `"iq"`, which performs protein quantification based on a maximal peptide ratio extraction algorithm that is adapted from the MaxLFQ algorithm of the MaxQuant software. Functions from the `iq` package are used. Default is `"iq"`.
`for_plot`	A logical indicating whether the result should be only protein intensities or protein intensities together with precursor intensities that can be used for plotting using `qc_protein_abundance`. Default is `FALSE`.
`retain_columns`	A vector indicating if certain columns should be retained from the input data frame. Default is not retaining additional columns `retain_columns = NULL`. Specific columns can be retained by providing their names (not in quotations marks, just like other column names, but in a vector).

Value

If for_plot = FALSE, protein abundances are returned, if for_plot = TRUE also precursor intensities are returned. The later output is ideal for plotting with qc_protein_abundance and can be filtered to only include protein abundances.

Examples

## Not run: 
calculate_protein_abundance(
  data,
  sample = r_file_name,
  protein_id = pg_protein_accessions,
  precursor = eg_precursor_id,
  peptide = pep_stripped_sequence,
  intensity_log2 = normalised_intensity_log2,
  method = "iq",
  retain_columns = c(pg_protein_accessions)
)

## 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