K2tax: Function to K2 Taxonomer partitioning

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

Function to K2 Taxonomer partitioning

Description

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

Usage

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

Arguments

K2res	A K2 class object.
nFeats	'sqrt' or a numeric value <= number of features to subset for each partition.
featMetric	Character. Metric to use to assign gene-level variance/signal score. F: F-statistic from evaluating differences in means across cohort mad: Median absolute deviation sd: Standard deviation Sn: Robust scale estimator
recalcDataMatrix	Logical. Recalculate dataMatrix for each partion? Default is TRUE.
nBoots	nBoots A value of the number of bootstraps to run at each partition. Default is 500.
clustFunc	Character. Wrapper function to be used in recursive partitioning. cKmeansDownsampleSqrt: Perform constrained K-means clustering after subsampling each cohort by the square root of the number of observations cKmeansDownsampleSmallest: Perform constrained K-means clustering after subsampling each cohort by the size of the smallest cohort hclustWrapper: Perform hierarchical clustering
useCors	Numeric. Number of cores to use for parallelizable processes.
clustList	Optional named list of parameters to use with clustFunc. cKmeansDownsampleSqrt: maxIter: The maximum number of iterations to use with lcvqe() cKmeansDownsampleSmallest: maxIter: The maximum number of iterations to use with lcvqe() hclustWrapper: aggMethod: One of the hierarchichal methods specified by hclust() function distMetric: One of the distance metrics specified by dist() function
linkage	Character. Linkage criteria for splitting cosine matrix ('method' in hclust). 'average' by default.
oneoff	Logical. Allow 1 observation partition groups? Default is TRUE.
stabThresh	Numeric. A value between 0 and 1 indicatingThreshold for ending clustering.

Value

An object of class K2.

References

\insertRef

reed_2020K2Taxonomer

montilab/K2Taxonomer documentation built on April 5, 2025, 3:58 a.m.