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Data.frame to QFeatures object conversion by parsing column names

make_pe_parse.Rd

make_pe_parse creates a QFeatures object based on a single data.frame. The experiment design is constructed by colnames of expression assay.

Usage

make_pe_parse(
  Peptide,
  columns,
  fnames,
  mode = c("char", "delim"),
  chars = 1,
  sep = "_",
  remove_prefix = T,
  remove_suffix = F,
  assay_name = "peptideRaw",
  log2transform = T
)

Arguments

Peptide

Data.frame, Peptide table with its belonging proteingroup.

columns

A numeric indicating the indices of the columns to be used as expression values. Can also be a character indicating the names of the columns.

fnames

An optional character(1) or numeric(1) indicating the column identifier.

mode

"char" or "delim", The mode of parsing the column headers. "char" will parse the last number of characters as replicate number and requires the 'chars' parameter. "delim" will parse on the separator and requires the 'sep' parameter.

chars

Numeric(1), The number of characters to take at the end of the column headers as replicate number (only for mode = "char").

sep

Character(1), The separator used to parse the column header (only for mode = "delim").

remove_prefix

Logical(1), whether remove the prefix of expression columns.

remove_suffix

Logical(1), whether remove the suffix of expression columns.

assay_name

An character(1) to name assay in the QFeatures object.

log2transform

Logical(1), whether log2 transform the assay, default TRUE.

Value

An character(1) to name assay in the QFeatures object.

Examples

# Load a peptides
data(Silicosis_peptide)
ecols <- grep("Intensity.", colnames(Silicosis_peptide), value = TRUE)
# Construct a QFeatures object, with a 'peptideRaw' assay
pe_peptides <- make_pe_parse(Silicosis_peptide, columns = ecols,   # columns is the abundance columns
                             mode = "delim", sep = "_",
                             remove_prefix = TRUE, log2transform = TRUE)
pe_peptides
#> An instance of class QFeatures containing 1 assays:
#>  [1] peptideRaw: SummarizedExperiment with 143528 rows and 20 columns