Normalize a QFeatures object — normalize

Normalize the i assay in QFeatures object though QFeatures::normalize function. The normalized assay is saved in the name assay.

Usage

normalize_pe(
  pe,
  method = c("diff.median", "quantiles", "quantiles.robust", "vsn"),
  i = "peptideImp",
  name = "peptideNorm"
)

Arguments

pe: A QFeature object
method: Character(1), normalisation method, one of "diff.median", "quantiles", "quantiles.robust" or "vsn". See normalize.
i: A numeric or a character giving the index or the name, respectively, of the assay(s) to be processed.
name: Character(1) naming the new normalized assay.

Examples

if (FALSE) {
# Load example peptide data
data(Silicosis_peptide)
ecols <- grep("Intensity.", colnames(Silicosis_peptide), value = TRUE)

# Construct QFeature object
pe_peptides <- make_pe_parse(Silicosis_peptide, columns = ecols, remove_prefix = TRUE, log2transform = TRUE,mode = "delim")

# Filter, imputation
pe <- filter_pe(pe_peptides, thr = 1,fraction = 0.4, filter_formula = ~ Reverse != '+' & Potential.contaminant !="+" )
pe <- impute_pe(pe, fun = "QRILC", name = "peptideImp")

# Normalization
pe <- normalize_pe(pe,method = "quantiles", i = "peptideImp", name = "peptideNorm")
}