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
|
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)