Export Data to CSV file — save_dataset

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

Usage

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

Arguments

data: MidarExperiment 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".
filter_data: A logical value indicating whether to use all data (default) or only QC-filtered data (filtered via filter_features_qc()).
qc_types: QC types to be plotted. Can be a vector of QC types or a regular expression pattern. NA (default) displays all available QC/Sample types.
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 FALSE 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, concorconc_raw, and TRUE` otherwise.
include_feature_filter: A character or regex pattern used to filter features by feature_id. If NA or an empty string ("") is provided, the filter is ignored. When a vector of length > 1 is supplied, only features with exactly these names are selected (applied individually as OR conditions).
exclude_feature_filter: A character or regex pattern used to exclude features by feature_id. If NA or an empty string ("") is provided, the filter is ignored. When a vector of length > 1 is supplied, only features with exactly these names are excluded (applied individually as OR conditions).
add_qctype: Add the QC type as column