read_maxquant_proteingroups: Read maxquant proteingroups

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Read maxquant proteingroups

Description

Read maxquant proteingroups

Usage

read_maxquant_proteingroups(
  dir = getwd(),
  file = if (is_file(dir)) dir else file.path(dir, "proteinGroups.txt"),
  fastafile = NULL,
  restapi = FALSE,
  quantity = NULL,
  subgroups = NULL,
  invert = character(0),
  contaminants = FALSE,
  reverse = FALSE,
  rm_missing_in_all_samples = TRUE,
  impute = FALSE,
  plot = FALSE,
  label = "feature_id",
  pca = plot,
  pls = plot,
  fit = if (plot) "limma" else NULL,
  formula = as.formula("~ subgroup"),
  block = NULL,
  coefs = NULL,
  contrasts = NULL,
  palette = NULL,
  verbose = TRUE
)

read_proteingroups(...)

Arguments

dir	proteingroups directory
file	proteingroups file
fastafile	uniprot fastafile
restapi	TRUE or FALSE : use uniprot restapi to annotate uniprots not in fastadt ?
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
impute	TRUE or FALSE: impute group-specific NA values?
plot	TRUE or FALSE: plot ?
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: character vector or NULL
contrasts	coefficient contrasts of interest: character vector or NULL
palette	color palette : named character vector
verbose	TRUE or FALSE : message ?
...	maintain deprecated functions

Value

SummarizedExperiment

Examples

# fukuda20 - LFQ
    file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
    pro <- read_maxquant_proteingroups(file = file)
    
# billing19 - Normalized Ratios
         file <- system.file('extdata/billing19.proteingroups.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 = file, subgroups = subgroups)
    pro <- read_maxquant_proteingroups(file = file, fastafile = fastafile, subgroups = subgroups)

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.