Skip to contents

Export Data to CSV file

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

This function exports specific unprocessed or pr ocessed 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,
  filter_data = FALSE,
  qc_types = NA,
  include_qualifier = NA,
  include_istd = NA,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  add_qctype = NA
)

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".

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.

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

See also

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