protti: qc_median_intensities – R documentation

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qc_median_intensities

Median run intensities

Median intensities per run are returned either as a plot or a table.

qc_median_intensities(
  data,
  sample,
  grouping,
  intensity,
  plot = TRUE,
  interactive = FALSE
)

`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 precursor or peptide identifiers.
`intensity`	the name of the column containing intensity values. The intensity should be ideally log2 transformed, but also non-transformed values can be used.
`plot`	logical, if TRUE a plot is returned. If FALSE a table is returned.
`interactive`	logical, if TRUE the plot is interactive using plotly.

A plot that displays median intensity over all samples. If plot = FALSE a data frame containing median intensities is returned.

## Not run: 
qc_median_intensities(
  data,
  sample = r_file_name,
  grouping = eg_precursor_id,
  intensity = log2_intensity
)

## End(Not run)

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