clustWspillOver {ADAPTS}R Documentation

Cluster with spillover

Description

Build clusters based on n-pass spillover matrix

Usage

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

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)

Value

Cell types grouped by cluster

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)

[Package ADAPTS version 1.0.6 Index]