View source: R/3.0_read_omics.R
sumexplist_to_longdt | R Documentation |
SummarizedExperiment list to long data.table
sumexplist_to_longdt(
sumexplist,
svars = intersect("subgroup", autonomics::svars(sumexplist[[1]])),
fvars = intersect("gene", autonomics::fvars(sumexplist[[1]])),
setvarname = "set"
)
sumexplist |
list of SummarizedExperiments |
svars |
character vector |
fvars |
character vector |
setvarname |
string |
data.table
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'))
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