protti: qc_intensity_distribution – R documentation

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protti

qc_intensity_distribution

Check intensity distribution per sample and overall

Description

Plots the overall or sample-wise distribution of all peptide intensities as a boxplot or histogram.

Usage

qc_intensity_distribution(
  data,
  sample = NULL,
  grouping,
  intensity_log2,
  plot_style
)

Arguments

`data`	A data frame containing at least sample names, grouping identifiers (precursor, peptide or protein) and log2 transformed intensities for each grouping identifier.
`sample`	The column in the data frame containing the sample name. NOTE: If the overall distribution should be returned please do not provide the name of the sample column.
`grouping`	The column in the data frame containing either precursor, peptide or protein identifiers.
`intensity_log2`	The column in the data frame containing the log2 transformed intensities of each grouping identifier sample combination.
`plot_style`	A character vector indicating the plot type. This can be either "histogram", "boxplot" or "violin". Plot style "boxplot" and "violin" can only be used if a sample column is provided.

Value

A histogram or boxplot that shows the intensity distribution over all samples or by sample.

Examples

## Not run: 
qc_intensity_distribution(
  data,
  sample = r_file_name,
  grouping = eg_precursor_id,
  intensity_log2 = normalised_intensity_log2,
  plot_style = "boxplot"
)

## 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

qc_intensity_distribution

Description

Usage

Arguments

Value

Examples

protti

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