read_maxquant_phosphosites: Read maxquant phosphosites

In bhagwataditya/autonomics: Unified statistal Modeling of Omics Data

Read maxquant phosphosites

Description

Read maxquant phosphosites

Usage

read_maxquant_phosphosites(
  dir = getwd(),
  fosfile = if (is_file(dir)) dir else file.path(dir, "phospho (STY)Sites.txt"),
  profile = file.path(dirname(fosfile), "proteinGroups.txt"),
  fastafile = NULL,
  restapi = FALSE,
  quantity = NULL,
  subgroups = NULL,
  invert = character(0),
  contaminants = FALSE,
  reverse = FALSE,
  rm_missing_in_all_samples = TRUE,
  localization = 0.75,
  impute = FALSE,
  plot = FALSE,
  label = "feature_id",
  pca = plot,
  pls = plot,
  fit = if (plot) "limma" else NULL,
  groupvar = "subgroup",
  formula = as.formula(sprintf("~ %s", groupvar)),
  block = NULL,
  coefs = NULL,
  contrasts = NULL,
  palette = NULL,
  verbose = TRUE
)

read_phosphosites(...)

Arguments

dir	proteingroups directory
fosfile	phosphosites file
profile	proteingroups file
fastafile	uniprot fastafile
restapi	TRUE or FALSE : annotate non-fastadt uniprots using uniprot restapi
quantity	'normalizedratio', 'ratio', 'correctedreporterintensity', 'reporterintensity', 'maxlfq', 'labeledintensity', 'intensity' or NULL
subgroups	NULL or string vector : subgroups to retain
invert	string vector: subgroups which require inversion
contaminants	TRUE or FALSE: retain contaminants ?
reverse	TRUE or FALSE: include reverse hits
rm_missing_in_all_samples	TRUE or FALSE
localization	number: min localization probability (for phosphosites)
impute	TRUE or FALSE: impute group-specific NA values?
plot	TRUE or FALSE
label	fvar
pca	TRUE or FALSE: run pca ?
pls	TRUE or FALSE: run pls ?
fit	model engine: 'limma', 'lm', 'lme(r)', 'wilcoxon' or NULL
formula	model formula
block	model blockvar: string or NULL
coefs	model coefficients of interest: string vector or NULL
contrasts	model coefficient contrasts of interest: string vector or NULL
palette	color palette: named string vector
verbose	TRUE or FALSE: message ?
...	maintain deprecated functions

Value

SummarizedExperiment

Examples

  profile <- system.file('extdata/billing19.proteingroups.txt', package = 'autonomics')
  fosfile <- system.file('extdata/billing19.phosphosites.txt',  package = 'autonomics')
fastafile <- system.file('extdata/uniprot_hsa_20140515.fasta',  package = 'autonomics')
subgroups <- sprintf('%s_STD', c('E00', 'E01', 'E02', 'E05', 'E15', 'E30', 'M00'))
pro <- read_maxquant_proteingroups(file = profile, subgroups = subgroups)
fos <- read_maxquant_phosphosites(fosfile = fosfile, profile = profile, subgroups = subgroups)
fos <- read_maxquant_phosphosites(fosfile = fosfile, profile = profile, fastafile = fastafile, subgroups = subgroups)

bhagwataditya/autonomics documentation built on Nov. 1, 2024, 5:47 a.m.