Function K2 Taxonomer

Source: R/K2tax.R

This function performs K2 Taxonomer procedure only. Arguments values are extracted from K2meta(K2res) unless othewise specified.

K2tax(
    K2res,
    nFeats = NULL,
    featMetric = NULL,
    recalcDataMatrix = NULL,
    nBoots = NULL,
    clustFunc = NULL,
    clustCors = NULL,
    clustList = NULL,
    linkage = NULL,
    oneoff = NULL,
    stabThresh = NULL
)

Arguments

K2res

An object of class K2. The output of K2preproc().
nFeats

A numeric value <= P of subsets of the data to use.
featMetric

Metric to use to assign variance/signal score. Options are 'square' (default), 'mad' to use MAD scores, 'sd' to use standard deviation
recalcDataMatrix

Recalculate dataMatrix for each partion?
nBoots

A numeric value of the number of bootstraps to run at each split.
clustFunc

Wrapper function to cluster a P x N (See details).
clustCors

Number of cores to use for clustering.
clustList

List of objects to use for clustering procedure.
linkage

Linkage criteria for splitting cosine matrix ('method' in hclust).
oneoff

Logical. Allow 1 member clusters?
stabThresh

A numeric value < 1, to set stopping threshold (use any negative value for no threshold).

Value

An object of class K2.

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)
data(sample.ExpressionSet)

## Pre-process and create K2 object
K2res <- K2preproc(sample.ExpressionSet)

## Run K2 Taxonomer algorithm
K2res <- K2tax(K2res,
            stabThresh=0.5)