protti: qc_proteome_coverage – R documentation

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qc_proteome_coverage

Proteome coverage per sample and total

Description

Calculates the proteome coverage for each samples and for all samples combined. In other words the fraction of detected proteins to all proteins in the proteome is calculated.

Usage

qc_proteome_coverage(
  data,
  sample,
  protein_id,
  organism_id,
  plot = TRUE,
  interactive = FALSE
)

Arguments

`data`	A data frame containing at least sample names and protein ID's.
`sample`	The column in the data data frame containing the sample name.
`protein_id`	The column in the data data frame containing protein identifiers such as UniProt accessions.
`organism_id`	The NCBI taxonomy identifier (TaxId) of the organism used. Human: 9606, S. cerevisiae: 559292, E. coli: 83333.
`plot`	A logical indicating whether the result should be plotted (default is TRUE).
`interactive`	A logical indicating whether the plot should be interactive (default is FALSE).

Value

A bar plot showing the percentage of of the proteome detected and undetected in total and for each sample. If plot = FALSE a data frame containing the numbers is returned.

Examples

## Not run: 
qc_proteome_coverage(
  data,
  sample = r_file_name,
  protein_id = pg_protein_accession,
  organism_id = 9606
)

## 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