sumexp_to_wide_dt {autonomics} | R Documentation |
Convert SummarizedExperiment into data.table
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)
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) |
sumexp_to_wide_dt
: feature x sample
sumexp_to_subrep_dt
: feature.subgroup x replicate
sumexp_to_long_dt
: feature.sample
data.table
# 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)