spillToConvergence {ADAPTS}R Documentation

Spillover to convergence

Description

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

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

Usage

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

method

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

Value

A list of signature matrices

Examples

#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)

[Package ADAPTS version 1.0.6 Index]