Reformats the output of K2tax() to an object of class, dendrogram, which can be easily plotted.

K2dendro(K2res)

Arguments

K2res

An object of class K2. The output of K2tax().

Value

An object of class dendrogram.

References

Reed ER, Monti S (2020). “Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.” Bioinformatics. doi: 10.1101/2020.11.05.370197 , http://biorxiv.org/lookup/doi/10.1101/2020.11.05.370197.

Examples

## Read in ExpressionSet object library(Biobase)
#> 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 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, colnames, #> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, #> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, #> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, #> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, #> union, unique, unsplit, which.max, which.min
#> Welcome to Bioconductor #> #> Vignettes contain introductory material; view with #> 'browseVignettes()'. To cite Bioconductor, see #> 'citation("Biobase")', and for packages 'citation("pkgname")'.
data(sample.ExpressionSet) ## Pre-process and create K2 object K2res <- K2preproc(sample.ExpressionSet) ## Run K2 Taxonomer algorithm K2res <- K2tax(K2res, stabThresh=0.5) ## Create dendrogram object from K2 Taxonomer results K2dendro(K2res)
#> 'dendrogram' with 2 branches and 26 members total, at height 4.381646