sumexplist_to_longdt: SummarizedExperiment list to long data.table

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

SummarizedExperiment list to long data.table

Description

SummarizedExperiment list to long data.table

Usage

sumexplist_to_longdt(
  sumexplist,
  svars = intersect("subgroup", autonomics::svars(sumexplist[[1]])),
  fvars = intersect("gene", autonomics::fvars(sumexplist[[1]])),
  setvarname = "set"
)

Arguments

sumexplist	list of SummarizedExperiments
svars	character vector
fvars	character vector
setvarname	string

Value

data.table

Examples

subgroups <- paste0(c('E00', 'E01', 'E02', 'E05', 'E15', 'E30', 'M00'), '_STD')
rnafile <- system.file('extdata/billing19.rnacounts.txt',     package = 'autonomics')
profile <- system.file('extdata/billing19.proteingroups.txt', package = 'autonomics')
fosfile <- system.file('extdata/billing19.phosphosites.txt',  package = 'autonomics')
rna <- read_rnaseq_counts(rnafile)
pro <- read_maxquant_proteingroups(file = profile, subgroups = subgroups)
fos <- read_maxquant_phosphosites(fosfile = fosfile, profile = profile, subgroups = subgroups)
pro$subgroup %<>% stringi::stri_replace_first_fixed('_STD', '')
fos$subgroup %<>% stringi::stri_replace_first_fixed('_STD', '')
    
sumexplist <- list(rna = rna, pro = pro, fos = fos)
dt <- sumexplist_to_longdt(sumexplist, setvarname = 'platform')
dt %<>% extract(gene %in% c('TNMD', 'TSPAN6'))

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