AccuCor2 - Isotope Natural Abundance Correction for dual-isotope data

AccuCor2 is an isotope natural abundance correction algorithm for dual-isotope experimental data. AccuCor2 supports 13C-2H and 13C-15N isotope correction.

AccuCor2 accepts Excel (.xls and .xlsx) files.

Installation

Download R to install accucor2.

# Please make sure all the required packages are updated.
install.packages("devtools")
library(devtools)
devtools::install_github("wangyujue23/AccuCor2",INSTALL_opts = "--no-multiarch")

Usage

library(accucor2)

# Example for 13C-15N tracer data:
# Input file and the Sheet name (example file included)
# Or use your own: input_file <- "/path/to/my/datafile.xlsx"
# You may use the example files in the "inst/extdata" folder as a template to format your own data.

input_file <- system.file("extdata", "CN_Compound_Test.xlsx", package = "accucor2")
sheet_name <- "Sheet1"
metabolite_list <-system.file("extdata", "Metabolite Formula and Charge Info.csv", package = "accucor2")

# Be sure to specify the appropriate resolution.
# For Exactive, the resolution is 70000, defined at 200 Mw
# Output is written into "corrected_[time].xlsx" under the directory folder by default (a message will show you where it is)
# The results are also returned as a named list of dataframes for further processing in R
# "Original", "Corrected", "Normalized", "Pool size"

corrected <- dual_correction(input_file,sheet_name,metabolite_list,"CN",Resolution = 70000)

corrected

# Example for 13C-2H tracer data:

input_file <- system.file("extdata", "CH_Compound_Test.xlsx", package = "accucor2")
sheet_name <- "Sheet1"
metabolite_list <-system.file("extdata", "Metabolite Formula and Charge Info.csv", package = "accucor2")

# The default value for tracer C/H/N isotopic purity is 0.99, you could change them by specify the value of C13Purity and H2N15Purity.
# You could also specify the natual abundance value. In this example, the NitrogenNaturalAbundace (14N, 15N) and SulfurNaturalAbundace (32S, 33S, 34S) are specified.

corrected <- dual_correction(input_file,sheet_name,metabolite_list,"CH",C13Purity = 1, H2N15Purity = 1, Resolution = 750000,NitrogenNaturalAbundance = c(0.99632, 0.00368),SulfurNaturalAbundance = c(0.9493, 0.0076, 0.0431))

corrected

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

Potential problem and solution

Error:

Warning in install.packages :
  download of package ‘utf8’ failed

Solution:

install.packages("utf8")