ADAPTS (version 0.9.21)

spillToConvergence: Build an n-pass spillover matrix, continuing until the results converge into clusters of cell types

Description

deconMatrices <- spillToConvergence(sigMatrix, geneExpr, 100, FALSE, TRUE)

Usage

spillToConvergence(sigMatrix, geneExpr, nPasses = 100, plotIt = FALSE,
  imputNAs = FALSE)

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 (DEFAULT: 100)

plotIt

Set to TRUE to plot it (DEFAULT: FALSE)

imputNAs

Set to TRUE to imput genes with missing values & cache the imputed. FALSE will just remove them (DEFAULT: FALSE)

Value

A list of signature matrices

Examples

# NOT RUN {
#This toy example 
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,] 

deconMatrices <- spillToConvergence(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10, plotIt=TRUE)
# }