diann_maxlfq: diann_maxlfq

diann_maxlfqR Documentation

diann_maxlfq

Description

Quantify using the MaxLFQ algorithm https://doi.org/10.1074/mcp.M113.031591. This function can be used to calculate protein quantities from peptide/precursor/fragment quantities or, for example, to calculate peptide quantities from precursor/fragment quantities. Totally based on function from diann-rpackage from Vadim Demichev

Usage

diann_maxlfq(
  x,
  sample.header = "File.Name",
  group.header = "Protein.Names",
  id.header = "Precursor.Id",
  quantity.header = "Precursor.Normalised",
  margin = -10,
  count_pep = TRUE,
  only_countsall = FALSE,
  Top3 = FALSE
)

Arguments

x

data, output from diann_load

sample.header

Sample id column name

group.header

Colulmn name corresponding to the group Id, e.g. protein Id

id.header

Id column name (protein, gene, ...)

quantity.header

Quantity column name

margin

quantities below exp(margin) might be treated as NA

count_pep

logical; get peptide count?

only_countsall

logical; should only keep peptide counts all or also peptide counts for each fractions?

Top3

logical; get Top3 absolute quantification

Value

A dataframe containing the quantities from the id you selected


mgerault/DIAgui documentation built on Nov. 7, 2024, 12:12 a.m.