Constructor for class adaptmle

Value

class adaptmle object, sub-classed from SummarizedExperiment.
Examples

library(SummarizedExperiment)
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:parallel’:
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following object is masked from ‘package:adaptest’:
#> 
#>     var
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
#>     colnames, colSums, dirname, do.call, duplicated, eval, evalq,
#>     Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
#>     lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
#>     pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
#>     rowSums, sapply, setdiff, sort, table, tapply, union, unique,
#>     unsplit, which, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:base’:
#> 
#>     expand.grid
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: DelayedArray
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘matrixStats’
#> The following objects are masked from ‘package:Biobase’:
#> 
#>     anyMissing, rowMedians
#> Loading required package: BiocParallel
#> 
#> Attaching package: ‘DelayedArray’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
#> The following objects are masked from ‘package:base’:
#> 
#>     aperm, apply
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)
Constructor for class adaptmle

Value

Examples

Contents
