data.file <- system.file("extdata", "Exp1_R25_pept.txt", package = "DaparToolshedData")

data <- read.table(data.file, header = TRUE, sep = "\t", as.is = TRUE, stringsAsFactors = FALSE)


qdata.indices <- 56:61
qdata.names <- colnames(data)[qdata.indices]


sample.file <- system.file("extdata", "samples_Exp1_R25.txt", package = "DaparToolshedData")

sample <- read.table(sample.file, header = TRUE, sep = " ", as.is = TRUE, stringsAsFactors = FALSE)


metacell.indices <- 43:48
metacell.names <- colnames(data)[metacell.indices]



ft <- createQFeatures(file = data.file,
  data = data, 
  sample = sample,
  indQData = 56:61,
  keyId = "Sequence",
  analysis = "test",
  logData = TRUE,
  indexForMetacell = as.numeric(43:48),
  typeDataset = "peptide",
  parentProtId = "Protein_group_IDs",
  force.na = TRUE,
  software = "maxquant"
  )


ft <- createQFeatures(file = data.file,
  data = data, 
  sample = sample,
  indQData = 56:61,
  keyId = "Sequence",
  analysis = "test",
  logData = TRUE,
  typeDataset = "peptide",
  parentProtId = "Protein_group_IDs",
  force.na = TRUE,
  software = "maxquant"
)




ft <- createQFeatures(file = data.file,
  data = data, 
  sample = sample,
  indQData = qdata.names,
  keyId = "Sequence",
  analysis = "test",
  indexForMetacell = metacell.names,
  typeDataset = "peptide",
  parentProtId = "Protein_group_IDs",
  force.na = TRUE,
  software = "maxquant")
