ADAPTS (version 1.0.22)

clustWspillOver: Cluster with spillover

Description

Build clusters based on n-pass spillover matrix

Usage

clustWspillOver(
  sigMatrix,
  geneExpr,
  nPasses = 100,
  deconMatrices = NULL,
  method = "DCQ"
)

Value

Cell types grouped by cluster

Arguments

sigMatrix

The deconvolution matrix, e.g. LM22 or MGSM27

geneExpr

The source gene expression matrix used to calculate sigMatrix.

nPasses

The maximum number of iterations for spillToConvergence (DEFAULT: 100)

deconMatrices

Optional pre-computed results from spillToConvergence (DEFAULT: NULL)

method

One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ)

Examples

#This toy example 
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,] 

clusters <- clustWspillOver(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10)