Get data frame from aggregated data

Retrieve a specific subset of the aggregated data into a single data frame by specifying which columns to take from each dataset (file_info, scans, peaks, etc.) using dplyr::select() syntax. If data from more than one dataset is selected (e.g. some columns from scans AND some from peaks), the datasets are combined with an dplyr::inner_join() using the columns listed in by (only the ones actually in the datasets). Joins that would lead to duplicated data entries (i.e. many-to-many joins) are not allowed and will throw an error to avoid unexpected replications of individual datapoints. If you really want to do such a join, you'll have to do it manually.

Usage

orbi_get_data(
  aggregated_data,
  file_info = c("filename"),
  scans = NULL,
  peaks = NULL,
  spectra = NULL,
  problems = NULL,
  summary = NULL,
  by = c("uidx", "scan.no")
)

Arguments

aggregated_data

datasets aggregated from orbi_aggregate_raw()

file_info

columns to get from the aggregated file_info, all dplyr::select() syntax is supported

scans

columns to get from the aggregated scans, all dplyr::select() syntax is supported

peaks

columns to get from the aggregated peaks, all dplyr::select() syntax is supported

spectra

columns to get from the aggregated spectra, all dplyr::select() syntax is supported

problems

columns to get from the aggregated problems, all dplyr::select() syntax is supported

summary

columns to get from the summary calculated via orbi_summarize_results(), all dplyr::select() syntax is supported. Warning: it is not advisable to combine columns from summary with anything other than file_info as it will lead to duplicated datasets given that summary integrates across multiple scans.

by

which columns to look for when joining datasets together. Make sure to include the relevant by columns in the selections of the individual datasets so they are joined correctly. The default is usually sufficient

Value

a tibble