Type: Package
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Version: 1.9.1
Depends: R (≥ 4.0)
Imports: IDSL.IPA (≥ 2.7), IDSL.UFA , readxl, RcppAlgos
Author: Sadjad Fakouri-Baygi ORCID iD [aut], Dinesh Barupal ORCID iD [cre, aut]
Maintainer: Dinesh Barupal <dinesh.barupal@mssm.edu>
Description: A pipeline to annotate a number of peaks from the 'IDSL.IPA' peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Si, N, H, As, F, I, Na, O, and P.
License: MIT + file LICENSE
URL: https://github.com/idslme/idsl.ufax
BugReports: https://github.com/idslme/idsl.ufax/issues
Encoding: UTF-8
Archs: i386, x64
NeedsCompilation: no
Packaged: 2023-04-04 13:11:19 UTC; sfbaygi
Repository: CRAN
Date/Publication: 2023-04-05 19:03:34 UTC

UFAx Workflow

Description

This function runs the exhaustive chemical enumeration part of the IDSL.UFAx pipeline.

Usage

UFAx_workflow(spreadsheet)

Arguments

spreadsheet

IDSL.UFAx parameter spreadsheet

Value

The MolecularFormulaAnnotationTable is saved in the assigned folder in the parameter spreadsheet.

Note

You should load the IDSL.UFA package to run the IDSL.UFAx functions.

Examples


library(IDSL.UFAx)
s_path <- system.file("extdata", package = "IDSL.UFAx")
SSh1 <- paste0(s_path,"/UFAx_parameters.xlsx")
temp_wd <- tempdir() # update this address
temp_wd_zip <- paste0(temp_wd,"/003.mzML_UFAx_testfiles.zip")
spreadsheet <- readxl::read_xlsx(SSh1)
download.file(
  paste0("https://github.com/idslme/IDSL.UFAx/blob/main/UFAx_educational_files/",
         "003.mzML_UFAx_testfiles.zip?raw=true"), destfile = temp_wd_zip, mode = "wb")
unzip(temp_wd_zip, exdir = temp_wd)
spreadsheet[1, 4] <- temp_wd
spreadsheet[3, 4] <- temp_wd
spreadsheet[6, 4] <- temp_wd
spreadsheet[5, 4] <- "seq(1, 100, 1)" # peak IDs to process
UFAx_results <- UFAx_workflow(spreadsheet)