diann_matrix: diann_matrix
In mgerault/DIAgui: A shiny app for processing DIAnn output in proteomics

diann_matrix

R Documentation

diann_matrix

Description

Generate matrix with quantities (zero will be replaced by NA values) and eventually peptides count.

Usage

diann_matrix(
  x,
  id.header = "Precursor.Id",
  quantity.header = "Precursor.Normalised",
  proteotypic.only = FALSE,
  q = 0.01,
  protein.q = 1,
  pg.q = 0.01,
  gg.q = 1,
  get_pep = FALSE,
  only_pepall = FALSE,
  margin = -10,
  Top3 = FALSE,
  method = c("max", "sum")
)

Arguments

`x`	data, output from diann_load
`id.header`	Id column name (protein, gene, ...)
`quantity.header`	Quantity column name
`proteotypic.only`	logical; Only proteotypic peptides and the respective proteins should be considered?
`q`	Precursor q-value threshold
`protein.q`	Uniquely identified protein q-value threshold
`pg.q`	Protein group q-value threshold
`gg.q`	Gene group q-value threshold
`get_pep`	logical; get peptide count?
`only_pepall`	logical; should only keep peptide counts all or also peptide counts for each fractions?
`margin`	quantities below exp(margin) might be treated as NA
`Top3`	logical; get Top3 absolute quantification
`method`	When for one identifier there are several values, take either maximum of these or sum them all. When using 'sum', any additional information than the id.header should be ignored. 'max' reports for only one id, 'sum' get the sum of the intensities of all ids.