nmr_integrate_regions: Integrate regions

In AlpsNMR: Automated spectraL Processing System for NMR

Description

Integrate given regions and return a data frame with them

Usage

nmr_integrate_regions(samples, regions, ...)

## S3 method for class 'nmr_dataset_1D'
nmr_integrate_regions(
  samples,
  regions,
  fix_baseline = TRUE,
  excluded_regions_as_zero = FALSE,
  set_negative_areas_to_zero = FALSE,
  ...
)

Arguments

samples	A nmr_dataset object
regions	A named list. Each element of the list is a region, given as a named numeric vector of length two with the range to integrate. The name of the region will be the name of the column
...	Keep for compatibility
fix_baseline	A logical. If TRUE it removes the baseline. See details below
excluded_regions_as_zero	A logical. It determines the behaviour of the integration when integrating regions that have been excluded. If TRUE, it will treat those regions as zero. If FALSE (the default) it will return NA values. If fix_baseline is TRUE, then the region boundaries are used to estimate a baseline. The baseline is estimated "connecting the boundaries with a straight line". Only when the spectrum is above the baseline the area is integrated (negative contributions due to the baseline estimation are ignored).
set_negative_areas_to_zero	A logical. Ignored if fix_baseline is FALSE. When set to TRUE negative areas are set to zero.

Value

An nmr_dataset_peak_table object

See Also

Other peak detection functions: Pipelines, nmr_baseline_threshold(), nmr_identify_regions_blood(), nmr_identify_regions_cell(), nmr_identify_regions_urine(), regions_from_peak_table(), validate_nmr_dataset_peak_table()

Other peak integration functions: Pipelines, computes_peak_width_ppm(), nmr_identify_regions_blood(), nmr_identify_regions_cell(), nmr_identify_regions_urine(), validate_nmr_dataset_peak_table()

Other nmr_dataset_1D functions: [.nmr_dataset_1D(), computes_peak_width_ppm(), file_lister(), files_to_rDolphin(), format.nmr_dataset_1D(), is.nmr_dataset_1D(), load_and_save_functions, new_nmr_dataset_1D(), nmr_align_find_ref(), nmr_baseline_removal(), nmr_baseline_threshold(), nmr_exclude_region(), nmr_interpolate_1D(), nmr_meta_add(), nmr_meta_export(), nmr_meta_get_column(), nmr_meta_get(), nmr_normalize(), nmr_pca_build_model(), nmr_pca_outliers_filter(), nmr_pca_outliers_plot(), nmr_pca_outliers_robust(), nmr_pca_outliers(), nmr_ppm_resolution(), plot.nmr_dataset_1D(), plot_webgl(), print.nmr_dataset_1D(), rdCV_PLS_RF_ML(), rdCV_PLS_RF(), save_files_to_rDolphin(), to_ChemoSpec(), validate_nmr_dataset_peak_table(), validate_nmr_dataset()

Examples

#Creating a dataset
dataset <- new_nmr_dataset_1D(ppm_axis = 1:10,
                              data_1r = matrix(sample(0:99,replace = TRUE), nrow = 10),
                              metadata = list(external = data.frame(NMRExperiment = c("10", 
                              "20", "30", "40", "50", "60", "70", "80", "90", "100"))))

# Integrating selected regions
peak_table_integration = nmr_integrate_regions(
                                   samples = dataset,
                                   regions = list(ppm = c(2,5)),
                                   fix_baseline = TRUE)

#Creating a dataset
dataset <- new_nmr_dataset_1D(ppm_axis = 1:10,
                              data_1r = matrix(sample(0:99,replace = TRUE), nrow = 10),
                              metadata = list(external = data.frame(NMRExperiment = c("10",
                               "20", "30", "40", "50", "60", "70", "80", "90", "100"))))

# Integrating selected regions
peak_table_integration = nmr_integrate_regions(
                                   samples = dataset,
                                   regions = list(ppm = c(2,5)),
                                   fix_baseline = TRUE)
        

AlpsNMR documentation built on April 1, 2021, 6:02 p.m.