.read_maxquant {autonomics}R Documentation

Read/Analyze proteingroups/phosphosites

Description

Read/Analyze proteingroups/phosphosites

Usage

.read_maxquant(
  file,
  quantity = guess_maxquant_quantity(file),
  sfile = NULL,
  sfileby = NULL,
  subgroupvar = "subgroup",
  select_subgroups = NULL,
  invert_subgroups = character(0),
  pepcountpattern = MAXQUANT_PATTERNS_PEPCOUNTS[1],
  verbose = TRUE
)

read_proteingroups(
  file,
  quantity = guess_maxquant_quantity(file),
  sfile = NULL,
  sfileby = NULL,
  select_subgroups = NULL,
  contaminants = FALSE,
  reverse = FALSE,
  fastafile = NULL,
  invert_subgroups = character(0),
  impute = stri_detect_regex(quantity, "[Ii]ntensity"),
  pepcountpattern = MAXQUANT_PATTERNS_PEPCOUNTS[1],
  subgroupvar = NULL,
  formula = NULL,
  block = NULL,
  contrastdefs = NULL,
  pca = FALSE,
  fit = NULL,
  verbose = TRUE,
  plot = TRUE
)

read_phosphosites(
  file,
  proteinfile = paste0(dirname(file), "/proteinGroups.txt"),
  quantity = guess_maxquant_quantity(file),
  sfile = NULL,
  sfileby = NULL,
  select_subgroups = NULL,
  contaminants = FALSE,
  reverse = FALSE,
  min_localization_prob = 0.75,
  fastafile = NULL,
  invert_subgroups = character(0),
  pca = FALSE,
  fit = NULL,
  subgroupvar = NULL,
  formula = NULL,
  block = NULL,
  contrastdefs = NULL,
  verbose = TRUE,
  plot = TRUE
)

Arguments

file

proteingroups/phosphosites file

quantity

string: "Ratio normalized", "Ratio", "LFQ intensity", "Reporter intensity corrected", "Reporter intensity", "Intensity labeled", "Intensity"

sfile

sample file

sfileby

sample file mergeby column

subgroupvar

subgroup svar

select_subgroups

subgroups to be selected (character vector)

invert_subgroups

subgroups to be inverted (character vector)

pepcountpattern

value in MAXQUANT_PATTERNS_PEPCOUNTS

verbose

whether to message

contaminants

whether to return contaminants

reverse

whether to return reverse peptides

fastafile

NULL or fastafile (to deconvolute proteingroups)

impute

whether to impute consistent nondetects

formula

desgnmat formula

block

block svar

contrastdefs

contrastdef vector/matrix/list

pca

whether to pca

fit

fit model: NULL, 'limma', 'lm', 'lme', 'lmer','wilcoxon'

plot

whether to plot

proteinfile

proteingroups file

min_localization_prob

min site localization probability (number)

Value

SummarizedExperiment

Examples

file <- download_data('fukuda20.proteingroups.txt')
object <- read_proteingroups(file, pca=TRUE, fit='limma')

[Package autonomics version 1.2.0 Index]