Constructor for class adaptmle
class adaptmle
object, sub-classed from SummarizedExperiment.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | library(SummarizedExperiment)
library(airway)
data(airway)
example_adaptmle_class <- function(se, n_top = 20, n_fold = 10) {
call <- match.call(expand.dots = TRUE)
adaptmle <- .adaptmle(
SummarizedExperiment::SummarizedExperiment(
assays = SummarizedExperiment::assay(se),
colData = SummarizedExperiment::colData(se)
),
call = call,
folds = list(), # folds (from origami)
plot_ingredients = list(), # top_colname
diff_exp = as.numeric(rep(NaN, n_top)), # DE
p_value = as.numeric(rep(NaN, n_top)), # p_value
q_value = as.numeric(rep(NaN, n_top)), # q_value
q_sig = as.numeric(rep(NaN, n_top)), # significant_q
q_sig_names = list(), # top_colname_significant_q
rank_mean = as.numeric(rep(NaN, n_top * n_fold)), # mean_rank_top
prob_top = as.numeric(rep(NaN, n_top * n_fold)), # prob_in_top
top_index = as.numeric(rep(NaN, n_top * n_fold)) # top_index
)
return(adaptmle)
}
example_class <- example_adaptmle_class(se = airway)
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