diann_maxlfq: Quantify using the MaxLFQ algorithm...

In vdemichev/diann-rpackage: Report processing and protein quantification for MS-based proteomics

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.

Usage

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

Arguments

x	data frame or data table
sample.header	sample Id column name
group.header	column name corresponding to the group Id, e.g. protein Id
id.header	precursor/peptide Id column name
quantity.header	precursor/peptide quantity column name
margin	quantities below exp(margin) might be treated as NA

Examples

df <- data.frame(File.Name = c("A","A","A","B","B","B"),Protein.Names=rep("ALB",6),
      Precursor.Id=rep(c("PEPTIDE","EPTIDEP","PTIDEPE"),2),Precursor.Normalised=c(20,10,5,25,12,NA))
diann_maxlfq(df)

vdemichev/diann-rpackage documentation built on May 11, 2020, 12:57 p.m.