applySimplePPT: Applies the Simple PPT algorithm onto the expression data.

Description Usage Arguments Value

View source: R/TreeBasedMethods.R

Description

Applies the Simple PPT algorithm onto the expression data.

Usage

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applySimplePPT(
  exprData,
  numCores,
  permExprData = NULL,
  nNodes_ = round(sqrt(nrow(exprData))),
  sigma = 0,
  gamma = 0
)

Arguments

exprData

Expression data – Num_Genes x Num_Samples

numCores

Number of cores to use during this analysis

permExprData

a list of permutated expression datasets, to use for significance estimation of the tree [default:NULL]

nNodes_

Number of nodes to find. Default is sqrt(N)

sigma

regularization parameter for soft-assignment of data points to nodes, used as the variance of a guassian kernel. If 0, this is estimated automatically

gamma

graph-level regularization parameter, controlling the tradeoff between the noise-levels in the data and the graph smoothness. If 0, this is estimated automatically.

Value

Information on the fitten tree


YosefLab/VISION documentation built on Sept. 14, 2021, 5:27 p.m.