IPA_xlsxAnalyzer: IPA xlsx Analyzer

In IDSL.IPA: Intrinsic Peak Analysis (IPA) for HRMS Data

IPA xlsx Analyzer

Description

This function processes the spreadsheet of the IPA parameters to ensure the parameter inputs are in agreement with the IPA requirements.

Usage

IPA_xlsxAnalyzer(spreadsheet)

Arguments

spreadsheet

IPA spreadsheet

Value

This function returns the IPA parameters to feed the IPA_Workflow, IPA_CompoundsAnnotation, IPA_GapFiller, IPA_PeakAlignment, IPA_PeakAnalyzer, and IPA_PeaklistAnnotation functions.

Examples

s_path <- system.file("extdata", package = "IDSL.IPA")
SSh1 <- paste0(s_path, "/IPA_parameters.xlsx")
temp_wd <- tempdir()
temp_wd_zip <- paste0(temp_wd,"/idsl_ipa_test_files.zip")
spreadsheet <- readxl::read_xlsx(SSh1)
PARAM = cbind(spreadsheet[, 2], spreadsheet[, 4])
tryCatch({download.file(paste0("https://github.com/idslme/IDSL.IPA/blob/main/",
                     "IPA_educational_files/idsl_ipa_test_files.zip?raw=true"),
              destfile = temp_wd_zip)
unzip(temp_wd_zip, exdir = temp_wd)
pass_download <- TRUE},
error = function(e) {pass_download <- FALSE},
warning = function(w) {pass_download <- FALSE})
if (pass_download) {
  PARAM[7, 2] <- temp_wd
  PARAM[10, 2] <- temp_wd # output data location
  PARAM[44, 2] <- s_path # reference file location
  PARAM <- IDSL.IPA::IPA_xlsxAnalyzer(PARAM)
}

IDSL.IPA documentation built on June 7, 2023, 6:01 p.m.