report_process: report_process

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

report_process

Description

Process data from DIAnn in a single workflow, save it and also save some quality check plots.

Usage

report_process(
  data,
  header.id = "Protein.Group",
  sample.id = "File.Name",
  quantity.id = "Precursor.Normalised",
  secondary.id = "Precursor.Id",
  id_to_add = c("Protein.Names", "First.Protein.Description", "Genes"),
  qv = 0.01,
  pg.qv = 0.01,
  p.qv = 1,
  gg.qv = 1,
  only_proteotypic = TRUE,
  get_pep = TRUE,
  only_pepall = FALSE,
  get_Top3 = FALSE,
  get_iBAQ = FALSE,
  fasta = NULL,
  species = NULL,
  peptide_length = c(5, 36),
  format = c("xlsx", "csv", "txt")
)

Arguments

data	Path to data (report from DIAnn)
header.id	Id column name (protein, gene, ...)
sample.id	Id column that contains the fractions names
quantity.id	Quantity column name (Precursor.Normalised)
secondary.id	Id column that contains precursor (usefull when get_pep is TRUE)
id_to_add	Some secondary id you want to keep in your final data
qv	Precursor q-value threshold
pg.qv	Protein group q-value threshold
p.qv	Uniquely identified protein q-value threshold
gg.qv	Gene group q-value threshold
only_proteotypic	If TRUE, will only keep proteotypic
get_pep	logical; get peptide count ?
only_pepall	logical; should only keep peptide counts all or also peptide counts for each fractions ?
get_Top3	If TRUE, will calculate Top3 quantification (only use when header.id is set to 'Protein.group' or 'Genes)
get_iBAQ	If TRUE, will calculate iBAQ quantification (only use when header.id is set to 'Protein.group' )
fasta	When iBAQ is set to TRUE, you can add path to fasta files. If NULL, will get theoretical peptides from swissprot bank (quite long).
species	When fasta is NULL, you need to specify the specie from your data
peptide_length	The minimum and maximum peptide length
format	Format from your saved file (only xlsx, csv and txt are supported)

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