protti: qc_data_completeness – R documentation

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qc_data_completeness

Data completeness

Description

Calculates the percentage of data completeness. That means, what percentage of all detected precursors is present in each sample.

Usage

qc_data_completeness(
  data,
  sample,
  grouping,
  intensity,
  digestion = NULL,
  plot = TRUE,
  interactive = FALSE
)

Arguments

`data`	A data frame containing at least the input variables.
`sample`	The name of the column containing the sample names.
`grouping`	The name of the column containing either precursor or peptide identifiers.
`intensity`	The name of the column containing any intensity intensity values that missingness should be determined for.
`digestion`	Optional column indicating the mode of digestion (limited proteolysis or tryptic digest). Alternatively, any other variable by which the data should be split can be provided.
`plot`	Logical, if TRUE a plot is returned. If FALSE a table is returned.
`interactive`	Logical, if TRUE the plot is interactive using plotly.

Value

A bar plot that displays the percentage of data completeness over all samples. If plot = FALSE a data frame is returned. If interactive = TRUE, the plot is interactive.

Examples

## Not run: 
qc_data_completeness(
  data,
  sample = r_file_name,
  grouping = eg_precursor_id,
  intensity = fg_quantity,
  digestion = digestion
)

## 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