IPA_xlsxAnalyzer {IDSL.IPA}

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)
}