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

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)

[Package autonomics version 1.2.0 Index]