compute_protein_number: Compute protein abundance using the protein ruler methodology

In VoisinneG/proteinRuler: proteinRuler

Compute protein abundance using the protein ruler methodology

Description

Compute protein abundance using the protein ruler methodology

Usage

compute_protein_number(
  df,
  idx_histones,
  pattern_intensity = "^Intensity.",
  col_intensity = NULL,
  col_mass = "Mass",
  col_ID = names(df)[1],
  mass_per_cell_in_g = NULL,
  DNA_mass_per_cell = 5.5209e-12,
  replace_zero_by_na = TRUE
)

Arguments

df	A data.frame containing protein intensities. By default, protein intensity column names start by "Intensity." (use parameter pattern_intensity to change)
idx_histones	Row indexes corresponding to histone proteins
pattern_intensity	Pattern (regular exrpression) used to identfy df's columns containing protein intensity values
col_intensity	Names of intensity columns. Overrides pattern_intensity.
col_mass	Column with protein mass (in kDa)
col_ID	Column with IDs
mass_per_cell_in_g	Compute protein abundance using a constant mass per cell (in g).
DNA_mass_per_cell	Mass of DNA per cell (in g)
replace_zero_by_na	Replace zero-valued intensities by NA.

Value

a list containing the following elements :

copy_number : a data.frame with protein abundances

summary : a data.frame with summary variables

Examples

## Not run: 
data("proteinGroups_CD4_Tcells")
idx_h <- grep("^Histone H", proteinGroups_CD4_Tcells$`Protein names`)
col_mass <- "Mol. weight [kDa]"
res <- compute_protein_number(proteinGroups_CD4_Tcells, 
idx_histones = idx_h, 
col_mass = col_mass)

## End(Not run)

VoisinneG/proteinRuler documentation built on Oct. 13, 2022, 9:47 p.m.