proteinRuler: 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

proteinRuler(
  df,
  col_protein_id = "Protein IDs",
  sep_id = ";",
  pattern_intensity = "^Intensity.",
  col_intensity = NULL,
  mass_per_cell_in_g = NULL,
  DNA_mass_per_cell = 5.5209e-12,
  filtering = TRUE,
  col_names = "Gene names",
  col_score = "Score",
  Score_threshold = 0,
  idx_histones = NULL,
  col_mass = NULL,
  show_progress = TRUE,
  replace_zero_by_na = TRUE,
  max_keys = 200,
  ...
)

Arguments

df	A data.frame containing protein intensities. By default, protein intensity column names start by "Intensity." (use parameter pattern_intensity to change)
col_protein_id	Column with protein IDs. When several protein IDs are found, only the first one is conserved.
sep_id	character string separating different protein IDs
pattern_intensity	Pattern (regular exrpression) used to identfy df's columns containing protein intensity values
col_intensity	Names of intensity columns. Overrides pattern_intensity.
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). Set to 5.5pg (corresponding to murine cells) by default
filtering	Filter out contaminants and poorly scored proteins.
col_names	Column with gene names.
col_score	Column with protein identification score
Score_threshold	Threshold on protein identification score
idx_histones	Row indexes corresponding to histone proteins. If NULL, histones are identified using UniProt annotations corresponding to the first ID of the protein group.
col_mass	Column with protein mass (in kDa). If NULL, protein mass are retireved from UniProt using the first ID of the protein group.
show_progress	Show progress bar when querrying annotations from UniProt
replace_zero_by_na	Replace zero-valued intensities by NA.
max_keys	Maximum query length used to retrieve UniProt data (passed to function pannot::get_annotations_uniprot())
...	additionnal parameters passed to fucntion pannot::get_annotations_uniprot()

Value

a data.frame with protein abundances

Examples

data("proteinGroups_CD4_Tcells")
res <- proteinRuler(proteinGroups_CD4_Tcells, DNA_mass_per_cell = 5.5209e-12)
str(res)
cond <- "CopyNumber_WT_0"
hist(log10(res$copy_number[[cond]]), main = "",
xlab = paste(cond, "(log10)"), col = rgb(1,0,0,0.25))

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