Import data from a TSV file created by MS-DIAL — import_from

Reads a tab-delimited peak table (TSV) exported from MS-DIAL. This works similarly to import_from_excel, but removes the need to manually open and re-save the TSV files in Excel. Excludes any summary statistics computed by MS-DIAL, such as average abundances, since these are not valid after notame processing.

Usage

import_from_msdial(
  file,
  id_column = NULL,
  id_prefix = "ID_",
  split_by = NULL,
  name = NULL,
  mz_limits = c(10, 2000),
  rt_limits = c(0, 20),
  skip_checks = FALSE
)

Arguments

file: path to the TSV file
id_column: character, column name for unique identification of samples
id_prefix: character, prefix for autogenerated sample IDs
split_by: character vector, in the case where all the modes are in the same Excel file, the column names of feature data used to separate the modes (usually Mode and Column)
name: in the case where the Excel file only contains one mode, the name of the mode, such as "Hilic_neg"
mz_limits: numeric vector of two, all m/z values should be in between these
rt_limits: numeric vector of two, all retention time values should be in between these
skip_checks: logical: skip checking and fixing of data integrity. Not recommended, but sometimes useful when you just want to read the data in as is and fix errors later. The data integrity checks are important for functioning of notame.

Value

A SummarizedExperiment with assays, rowData and colData filled from the TSV file.

Examples

# \donttest{
# Read a TSV peak table
# data <- import_from_msdial(file = "path/to/peak_table.tsv", name = "RP_neg")
# }