DUBStepR (version 1.2.0)

getOptimalFeatureSet: Determine the optimal feature set using Density Index (DI)

Description

Determine the optimal feature set using Density Index (DI)

Usage

getOptimalFeatureSet(
  filt.data,
  ordered.genes,
  elbow.pt = 25,
  k = 10,
  num.pcs = 20,
  error = 0
)

Arguments

filt.data

log-transformed filtered gene-expression matrix

ordered.genes

genes ordered after stepwise regression

elbow.pt

Elbow point to start determining optimal feature set

k

number of nearest neighbours for CI computation

num.pcs

number of principal components to represent sc data. Default is 20.

error

Acceptable error margin for kNN computation. Default is 0, but is set to 1 for large datasets.

Value

optimal set of feature genes