protti: qc_peak_width – R documentation

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protti

qc_peak_width

Peak width over retention time

Description

Plots one minute binned median precursor elution peak width over retention time for each sample.

Usage

qc_peak_width(
  data,
  sample,
  intensity,
  retention_time,
  peak_width = NULL,
  retention_time_start = NULL,
  retention_time_end = NULL,
  remove_na_intensities = TRUE,
  interactive = FALSE
)

Arguments

`data`	A data frame containing at least sample names and protein IDs.
`sample`	The column in the data frame containing the sample names.
`intensity`	The column in the data frame containing intensities. If `remove_na_intensities = FALSE`, this argument is not required.
`retention_time`	The column in the data frame containing retention times of precursors.
`peak_width`	The column in the data frame containing peak width information. It is not required if `retention_time_start` and `retention_time_end` columns are provided.
`retention_time_start`	The column in the data frame containing the start time of the precursor elution peak. It is not required if the `peak_width` column is provided.
`retention_time_end`	The column in the data frame containing the end time of the precursor elution peak. It is not required if the `peak_width` column is provided.
`remove_na_intensities`	Logical specifying if sample/grouping combinations with intensities that are NA (not quantified IDs) should be dropped from the data frame. Default is TRUE since we are usually interested in the peak width of quantifiable data.
`interactive`	A logical indicating whether the plot should be interactive (default is FALSE).

Value

A line plot displaying one minute binned median precursor elution peak width over retention time for each sample.

Examples

## Not run: 
qc_peak_width(
  data,
  sample = r_file_name,
  intensity = fg_quantity,
  retention_time = eg_mean_apex_rt,
  retention_time_start = eg_start_rt,
  retention_time_end = eg_end_rt
)

## 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_peak_width

Description

Usage

Arguments

Value

Examples

protti

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