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Export data to a CSV file

Source: R/data-export.R
save_dataset_csv.Rd

This function exports specific unprocessed or processed feature variable (e.g. intensities or concentrations) from a MRMhubExperiment object to a CSV file. Allows selection of features and optional QC filtering.

Usage

save_dataset_csv(
  data = NULL,
  path,
  variable,
  qc_types = NA,
  filter_data = FALSE,
  include_qualifier = NA,
  include_istd = NA,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  add_qctype = NA,
  create_dir = TRUE
)

Arguments

data

MRMhubExperiment object

path

File name with path of exported CSV file

variable

Variable to be exported, must be present in the data and any of "area", "height", "intensity", "norm_intensity", "response", "conc", "conc_raw", "rt", "fwhm".

qc_types

QC types to be exported. Can be a vector of QC types or a regular expression pattern. NA (default) exports all available QC/Sample types.

filter_data

A logical value indicating whether to use all data (default) or only QC-filtered data (filtered via filter_features_qc()). Default is FALSE.

include_qualifier

A logical value indicating whether to include qualifier features. Default is NA, which will be automatically set to FALSE if variable is conc or conc_raw, and TRUE otherwise.

include_istd

A logical value indicating whether to include internal standard (ISTD) features. Default is NA, which will be automatically set to FALSE if variable is norm_intensity, conc or conc_raw, and TRUE otherwise.

include_feature_filter

Feature(s) to include by feature_id, as a character vector. Each element is matched exactly when it names an existing feature, otherwise treated as a regex; elements combine with OR. A full ID (e.g. "S1P d18:0 [M>60]") needs no escaping, while patterns like "PC|PE" still work. NA or "" ignores the filter.

exclude_feature_filter

Feature(s) to exclude by feature_id, matched the same way as include_feature_filter. NA or "" ignores the filter.

add_qctype

Add the QC type as column

create_dir

A logical value. If TRUE (the default), the parent directory of path is created if it does not yet exist.

See also

normalize_by_istd(), quantify_by_istd(), quantify_by_calibration(), calibrate_by_reference()