clustWspillOver: Cluster with spillover

In yxinyi2/ADAPTS1.0.3: Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

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)

yxinyi2/ADAPTS1.0.3 documentation built on Aug. 5, 2020, 12:09 a.m.