Prepares summarizedExperiment object to work with functions from DEP package.
Source:R/prepare_se.R
use_dep.Rd
Prepares summarizedExperiment object to work with functions from DEP package.
Arguments
- se
The summarizedExperiment object created with prepare_se
Examples
se <- prepare_se(report.pg_matrix, expDesign, report.pr_matrix)
#> Imputing along margin 2 (samples/columns).
#> [1] 0.3066195
#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#> mean imputation used for these rows
#> Cluster size 5574 broken into 3662 1912
#> Cluster size 3662 broken into 1462 2200
#> Done cluster 1462
#> Cluster size 2200 broken into 1110 1090
#> Done cluster 1110
#> Done cluster 1090
#> Done cluster 2200
#> Done cluster 3662
#> Cluster size 1912 broken into 1379 533
#> Done cluster 1379
#> Done cluster 533
#> Done cluster 1912
se_dep <- use_dep(se)