natural_abundance_correction: Natural Abundance correction for mass spectrometry data

In accucor: Natural Abundance Correction of Mass Spectrometer Data

Natural Abundance correction for mass spectrometry data

Description

natural_abundance_correction returns the corrected and normalized intensities of isotopically labeled mass spectrometry data. It was designed to work with input data from El-MAVEN and MAVEN software.

Usage

natural_abundance_correction(
  data,
  sheet = NULL,
  compound_database = NULL,
  output_base = NULL,
  output_filetype = "xlsx",
  columns_to_skip = NULL,
  resolution,
  resolution_defined_at = 200,
  purity = NULL,
  report_pool_size_before_df = FALSE,
  path = NULL
)

Arguments

data	Path to input data file (xlsx, xls, csv, txt, or tsv) OR dataframe. If dataframe is specified, specify output_base to output files automatically written.
sheet	Name of sheet in xlsx file with columns 'compound', 'formula', 'isotopelabel', and one column per sample. Defaults to the first sheet.
compound_database	Path to compound database in csv format. Only used for classic MAVEN style input when formula is not specified.
output_base	Path to basename of output file, default is the basename of the input path. '_corrected' will be appended. If 'FALSE' then no output file is written.
output_filetype	Filetype of the output file, one of: 'xls', xlsx', 'csv', or 'tsv'. The default is 'xlsx'.
columns_to_skip	Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names.
resolution	For Exactive, the resolution is 100000, defined at Mw 200
resolution_defined_at	Mw at which the resolution is defined, default 200 Mw
purity	Isotope purity, default: Carbon 0.99; Deuterium 0.98; Nitrogen 0.99
report_pool_size_before_df	Report PoolSizeBeforeDF, default = FALSE
path	Deprecated. Specify path to input data file (alias for 'data').

Details

C13, H2, and N15 isotopes are supported. The isotopes are detected from the isotopeLabel column of the input file. The expected label text is C13-label-#. D-label-#. or N15-label-#. Parent (unlabeled) compounds are specified by C12 PARENT.

Value

Named list of matrices: 'Corrected', 'Normalized', 'PoolBeforeDF', and 'PoolAfterDF'.

Examples

## Not run: 
natural_abundance_correction("inst/extdata/C_Sample_Input_Simple.xlsx",
  Resolution = 100000, ResDefAt = 200
)

## End(Not run)

accucor documentation built on Sept. 14, 2023, 5:09 p.m.