UFAx_workflow {IDSL.UFAx}

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)