preprocess mzMine input

Description

preprocess mzMine input

Usage

preprocess_mzMine(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = NULL,
  pattern_decoys = NULL,
  annotated = FALSE,
  nr_peptides = 1
)

Arguments

quant_data	path to mzMine features csv file
fasta_file	path to annotations csv file
annotation	annotation list from read_annotation
pattern_contaminants	regex pattern for contaminants
pattern_decoys	regex pattern for decoys
annotated	if TRUE only keep annotated features
nr_peptides	accepted for interface uniformity but ignored (mzMine features have one child per protein)

Value

A list containing the prepared LFQData and ProteinAnnotation objects.

Examples

library("prolfquapp")


if(FALSE){
xd <- "outputs-20250407T1707/bfabric/input_dataset.tsv"
annot <- readr::read_tsv(xd)

annotation <- read_annotation(annot, QC = TRUE)
xd <- "outputs-20250407T1707/"
files <- get_mzMine_files(path)
files
undebug(preprocess_mzMine)
res <- preprocess_mzMine(files$data, files$fasta , annotation)
dim(res$lfqdata$data)
res <- preprocess_mzMine(files$data, files$fasta , annotation, annotated = TRUE)
dim(res$lfqdata$data)
}