Skip to contents

Data.frame to QFeatures object conversion using an experimental design

make_pe.Rd

make_pe creates a QFeatures object based on two data.frames: the peptide table and experimental design.

Usage

make_pe(
  Peptide,
  columns,
  expdesign,
  fnames,
  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.

expdesign

A data.frame. Experimental design with 'label', 'condition' and 'replicate' information.

fnames

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

assay_name

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

log2transform

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

Value

A QFeatures object with a peptide assay.

Examples

# Load a peptides
data(Silicosis_peptide)
# Exctract Intensity columns
(ecols <- grep("Intensity.", colnames(Silicosis_peptide), value = TRUE))
#>  [1] "Intensity.PBS_1" "Intensity.PBS_2" "Intensity.PBS_3" "Intensity.PBS_4"
#>  [5] "Intensity.W10_2" "Intensity.W10_4" "Intensity.W2_1"  "Intensity.W2_3" 
#>  [9] "Intensity.W2_4"  "Intensity.W2_5"  "Intensity.W4_2"  "Intensity.W4_3" 
#> [13] "Intensity.W4_4"  "Intensity.W4_5"  "Intensity.W6_2"  "Intensity.W6_3" 
#> [17] "Intensity.W6_4"  "Intensity.W6_6"  "Intensity.W9_2"  "Intensity.W9_4" 


# Load experiement design
data(Silicosis_ExpDesign)
(expDesign = Silicosis_ExpDesign)
#>       label    ID condition replicate
#> PBS_1 PBS_1 PBS_1       PBS         1
#> PBS_2 PBS_2 PBS_2       PBS         2
#> PBS_3 PBS_3 PBS_3       PBS         3
#> PBS_4 PBS_4 PBS_4       PBS         4
#> W10_2 W10_2 W10_2       W10         2
#> W10_4 W10_4 W10_4       W10         4
#> W2_1   W2_1  W2_1        W2         1
#> W2_3   W2_3  W2_3        W2         3
#> W2_4   W2_4  W2_4        W2         4
#> W2_5   W2_5  W2_5        W2         5
#> W4_2   W4_2  W4_2        W4         2
#> W4_3   W4_3  W4_3        W4         3
#> W4_4   W4_4  W4_4        W4         4
#> W4_5   W4_5  W4_5        W4         5
#> W6_2   W6_2  W6_2        W6         2
#> W6_3   W6_3  W6_3        W6         3
#> W6_4   W6_4  W6_4        W6         4
#> W6_6   W6_6  W6_6        W6         6
#> W9_2   W9_2  W9_2        W9         2
#> W9_4   W9_4  W9_4        W9         4

# Construct a QFeatures object, with a 'peptideRaw' assay
pe_peptides <- make_pe(Silicosis_peptide, columns = ecols,   # columns is the abundance columns
                       expdesign = expDesign) # log2transform
pe_peptides # a QFeatures object, with a peptideRaw assay
#> An instance of class QFeatures containing 1 assays:
#>  [1] peptideRaw: SummarizedExperiment with 143528 rows and 20 columns