sumexp_to_wide_dt {autonomics}

R Documentation

Convert SummarizedExperiment into data.table

Description

Convert SummarizedExperiment into data.table

Usage

sumexp_to_wide_dt(
  object,
  fid = "feature_id",
  fvars = intersect("feature_name", autonomics::fvars(object)),
  assay = assayNames(object)[1]
)

sumexp_to_long_dt(
  object,
  fid = "feature_id",
  fvars = intersect("feature_name", autonomics::fvars(object)),
  sid = "sample_id",
  svars = intersect("subgroup", autonomics::svars(object)),
  assay = assayNames(object) %>% intersect(c(.[1], "is_imputed"))
)

sumexp_to_subrep_dt(object, subgroup = subgroup)

Arguments

object	sumexp
fid	fvar carrying feature id
fvars	additional fvars to include in table
assay	matrix in assays(object) to be used
sid	svar carrying sample id
svars	additional svars to include in table
subgroup	subgroup (sym)

Details

• sumexp_to_wide_dt: feature x sample

• sumexp_to_subrep_dt: feature.subgroup x replicate

• sumexp_to_long_dt: feature.sample

Value

data.table

Examples

# Stem cell comparison
    file <- download_data('billing16.proteingroups.txt')
    invert_subgroups <- c('EM_E', 'BM_E', 'EM_BM')
    object <- read_proteingroups(file, invert_subgroups = invert_subgroups,
                  plot=FALSE)
    sumexp_to_wide_dt(object)
    sumexp_to_long_dt(object)
    sumexp_to_subrep_dt(object)

# Glutaminase
   require(magrittr)
   file <- download_data('atkin18.metabolon.xlsx')
   object <- read_metabolon(file, plot=FALSE)
   sumexp_to_wide_dt(object)
   sumexp_to_long_dt(object)
   sumexp_to_subrep_dt(object, Group)

# Fukuda
   require(magrittr)
   file <- download_data('fukuda20.proteingroups.txt')
   object <- read_proteingroups(file, impute=FALSE, plot=FALSE)
   sumexp_to_long_dt(object)
   object %<>% impute_systematic_nondetects(plot=FALSE)
   sumexp_to_long_dt(object)

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