Package 'accucor'

accucor: A package for natural abundance correction of mass spectrometer data

Description

AccuCor is an isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. AccuCor supports correction for 13C, 2H and 15N.

AccuCor functions

natural_abundance_correction

Author(s)

Maintainer: Lance Parsons [email protected] (ORCID)

Authors:

• Xiaoyang Su [email protected] (ORCID)

Other contributors:

• Yujue Wang [email protected] (ORCID) [contributor]

• Princeton University [copyright holder]

See Also

Useful links:

• https://github.com/XiaoyangSu/AccuCor

• Report bugs at https://github.com/XiaoyangSu/AccuCor/issues

---

Natural Abundance carbon isotope correction for one metabolite

Description

Natural Abundance carbon isotope correction for one metabolite

Usage

carbon_isotope_correction(
  formula,
  datamatrix,
  label,
  Resolution,
  ResDefAt = 200,
  purity = 0.99,
  ReportPoolSize = TRUE
)

Arguments

formula	String representing molecular formula
datamatrix	Matrix of abundances for each sample for each isotope
label	vector of integer labels
Resolution	For Exactive, the Resolution is 100000, defined at Mw 200
ResDefAt	Resolution defined at (in Mw), e.g. 200 Mw
purity	Carbon 13 purity, default: 0.99
ReportPoolSize	default: TRUE

Value

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

Examples

## Not run: 
carbon_isotope_correction(
  formula = "C6H13O9P",
  datamatrix = DataMatrix,
  label = c(0, 1, 2, 3, 4, 5),
  Resolution = 100000
)

## End(Not run)

---

Standardize data frame columns and data types

Description

Standardize data frame columns and data types

Usage

clean_data_frame(df, columns_to_skip = NULL)

Arguments

df	Data frame to clean
columns_to_skip	Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names.

Value

"cleaned" data.frame which with columns 'compound', 'formula', 'isotope_label', label_index', followed by columns for each sample

---

Natural Abundance deuterium isotope correction for one metabolite

Description

Natural Abundance deuterium isotope correction for one metabolite

Usage

deuterium_isotope_correction(
  formula,
  datamatrix,
  label,
  Resolution,
  ResDefAt = 200,
  purity = 0.99,
  ReportPoolSize = TRUE
)

Arguments

formula	String representing molecular formula
datamatrix	Matrix of abundances for each sample for each isotope
label	vector of integer labels
Resolution	For Exactive, the Resolution is 100000, defined at Mw 200
ResDefAt	Resolution defined at (in Mw), e.g. 200 Mw
purity	Deuterium purity, default: 0.99
ReportPoolSize	default: TRUE

Value

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

Examples

## Not run: 
deuterium_isotope_correction(
  formula = "C6H13O9P",
  datamatrix = DataMatrix,
  label = c(0, 1),
  Resolution = 100000
)

## End(Not run)

---

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)

---

Natural Abundance deuterium isotope correction for one metabolite

Description

Natural Abundance deuterium isotope correction for one metabolite

Usage

nitrogen_isotope_correction(
  formula,
  datamatrix,
  label,
  Resolution,
  ResDefAt = 200,
  purity = 0.99,
  ReportPoolSize = TRUE
)

Arguments

formula	String representing molecular formula
datamatrix	Matrix of abundances for each sample for each isotope
label	vector of integer labels
Resolution	For Exactive, the Resolution is 100000, defined at Mw 200
ResDefAt	Resolution defined at (in Mw), e.g. 200 Mw
purity	Nitrogen purity, default: 0.99
ReportPoolSize	default: TRUE

Value

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

Examples

## Not run: 
nitrogen_isotope_correction(
  formula = "C23H38N7O17P3S",
  datamatrix = DataMatrix,
  label = c(0, 1, 2, 3, 4, 5, 6, 7),
  Resolution = 140000
)

## End(Not run)

---

Natural Abundance correction for Carbon labeled samples

Description

Natural Abundance correction for Carbon labeled samples

Usage

read_elmaven(
  path,
  sheet = NULL,
  compound_database = NULL,
  columns_to_skip = NULL,
  filetype = NULL,
  ...
)

Arguments

path	Path to input file.
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.
columns_to_skip	Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names.
filetype	Specify file type, default is to determine by file extension.
...	Pass additional parameters to readxl::read_excel

Value

List containing three items: "original" data.frame which is result of read_excel, "cleaned" data.frame which with columns 'compound', 'formula', 'isotope_label', label_index', followed by columns for each sample, and "isotope" which is a character indicating the isotope

Examples

## Not run: 
read_elmaven_xlsx("ExcelFile", "Sheet1")

## End(Not run)

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