sumexp_to_longdt: SummarizedExperiment to data.table

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

SummarizedExperiment to data.table

Description

SummarizedExperiment to data.table

Usage

sumexp_to_widedt(
  object,
  fvars = autonomics::fvars(object),
  assay = assayNames(object)[1]
)

sumexp_to_longdt(
  object,
  fvars = intersect("feature_name", autonomics::fvars(object)),
  svars = intersect("subgroup", autonomics::svars(object)),
  assay = assayNames(object) %>% intersect(c(.[1], "is_imputed"))
)

sumexp_to_subrep_dt(object, subgroup = subgroup)

Arguments

object	sumexp
fvars	additional fvars to include in table
assay	matrix in assays(object) to be used
svars	additional svars to include in table
subgroup	subgroup (sym)

Details

• sumexp_to_widedt: feature x sample

• sumexp_to_subrep_dt: feature.subgroup x replicate

• sumexp_to_longdt: feature.sample

Value

data.table

Examples

# Atkin Hypoglycemia
   file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
   object <- read_metabolon(file)
   sumexp_to_widedt(object)
   sumexp_to_longdt(object)
   sumexp_to_subrep_dt(object)

# Fukuda
   file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
   object <- read_maxquant_proteingroups(file)
   values(object)
   fdt(object)
   object %<>% impute()
   table(fdt(object)$imputed)
   sumexp_to_longdt(object)
   sumexp_to_widedt(object)
   sumexp_to_longdt(object)

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