clusteringLiger: LIGER clustering using iNMF or UINMF algorythm
In fpestana-git/clusteringR: Transcriptomic clustering functions

View source: R/clusteringLiger.R

clusteringLiger

R Documentation

LIGER clustering using iNMF or UINMF algorythm

Description

Function that takes a named list of datasets and integrates using LIGER

Usage

clusteringLiger(
  datasets,
  lambdaValue = 5,
  kValue = 25,
  referenceDatasetName,
  resolutionValue = 0.4,
  setVariableGenes = FALSE,
  variableGenes = NULL,
  num.genesValue = NULL,
  var.threshValue = 0.2,
  useiNMF = FALSE,
  useUINMF = FALSE,
  unshared.threshValue = NULL
)

Arguments

`datasets`	list of named datasets
`lambdaValue`	default 5
`kValue`	default 25
`referenceDatasetName`	name of dataset to use as reference dataset
`resolutionValue`	default 0.4
`setVariableGenes`	default FALSE
`variableGenes`	default NULL
`num.genesValue`	default NULL
`var.threshValue`	default 0.2
`useiNMF`	default FALSE
`useUINMF`	default FALSE
`unshared.threshValue`	default NULL