Extract the proteins SummarizedExperiment object from a QFeatures container

This function accept a result from aggregate_pe(), tidy features identifiers and return a SE object for following analyze

Usage

pe2se(
  pe_aggregated,
  names = "Gene.names",
  ids = "smallestProteingroups",
  delim = ";"
)

Arguments

pe_aggregated

A QFeatures object output from aggregate_pe(), which contain a "protein" quantative assay.

names

The column of gene names, which serve as feature identifier and is transmitted to make_unique

ids

The column of protein ID, transmitted to make_unique. aggregate_pe automatically generate a "smallestProteingroups" column to store ids in proteingroups.

delim

Character. The separator in names of ids.

Value

A SummarizedExperiment object.

Examples

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

# construct QFeatures 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")

# Summarize peptide value to protein quantity
protein_pe <- DEP2::aggregate_pe(pe, fcol = "Proteins", i = "peptideNorm")
class(protein_pe)

# Construct a SE object
se <- pe2se(protein_pe)
class(se)
}