createAutotuner: createAutotuner

In crmclean/Autotuner: Automated parameter selection for untargeted metabolomics data processing

Description

This function will create a Autotuner used to extract ms2s.

Usage

createAutotuner(data_paths, runfile, file_col, factorCol)

Arguments

data_paths	A string path pointing at data files to load in Autotuner.
runfile	A data.frame of sample metadata.
file_col	Character string of the column name of the column within the runfile that contains sample names.
factorCol	Character string of the column name of the column within the runfile that contains sample type factor.

Value

This function returns an Autotuner object

Examples

library(mtbls2)
rawPaths <- c(
system.file("mzData/MSpos-Ex2-cyp79-48h-Ag-1_1-B,3_01_9828.mzData",
package = "mtbls2"),
system.file("mzData/MSpos-Ex2-cyp79-48h-Ag-2_1-B,4_01_9830.mzData",
package = "mtbls2"),
system.file("mzData/MSpos-Ex2-cyp79-48h-Ag-4_1-B,4_01_9834.mzData",
package = "mtbls2"))

metadata <- read.table(system.file(
"a_mtbl2_metabolite_profiling_mass_spectrometry.txt", package = "mtbls2"),
header = TRUE, stringsAsFactors = FALSE)
metadata <- metadata[sub("mzData/", "",
metadata$Raw.Spectral.Data.File) %in% basename(rawPaths),]

Autotuner <- Autotuner::createAutotuner(rawPaths,
metadata,
file_col = "Raw.Spectral.Data.File",
factorCol = "Factor.Value.genotype.")

crmclean/Autotuner documentation built on Jan. 23, 2021, 1:43 a.m.