nmr_batman: Batman helpers

In AlpsNMR: Automated spectraL Processing System for NMR

Description

Batman helpers

Usage

nmr_batman_write_options(
  bopts,
  batman_dir = "BatmanInput",
  filename = "batmanOptions.txt"
)

nmr_batman_export_dataset(
  nmr_dataset,
  batman_dir = "BatmanInput",
  filename = "NMRdata.txt"
)

nmr_batman_multi_data_user_hmdb(
  batman_dir = "BatmanInput",
  filename = "multi_data_user.csv"
)

nmr_batman_multi_data_user(
  multiplet_table,
  batman_dir = "BatmanInput",
  filename = "multi_data_user.csv"
)

nmr_batman_metabolites_list(
  metabolite_names,
  batman_dir = "BatmanInput",
  filename = "metabolitesList.csv"
)

Arguments

bopts	Batman options
batman_dir	Batman input directorye
filename	Filename to use, inside batman_dir
nmr_dataset	An nmr_dataset_1D object
multiplet_table	A data frame, like the hmdb dataset
metabolite_names	A character vector of the metabolite names to consider

Value

These are helper functions to make Batman tests easier

See Also

Other batman functions: nmr_batman_options()

Examples

bopts <- nmr_batman_options()
# nmr_batman_write_options(bopts)

dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
#nmr_batman_export_dataset(dataset_1D)

message("Use of multi_data_user_hmdb")
#multi_data_user_hmdb <- nmr_batman_multi_data_user_hmdb()
hmdb <- NULL
#utils::data("hmdb", package = "AlpsNMR", envir = environment())
#hmdb <- nmr_batman_multi_data_user(hmbd)

metabolite_names <- c("alanine", "glucose")
#metabolite_names <- nmr_batman_metabolites_list(metabolite_names)

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