estCellCounts.nPass {ADAPTS}R Documentation

Deconvolve with an n-pass spillover matrix

Description

curExpr <- estCellCounts.nPass(sigMatrix, deconMatrices)

Usage

estCellCounts.nPass(geneExpr, deconMatrices, method = "DCQ")

Arguments

geneExpr

The gene expression matrix

deconMatrices

The results from spillToConvergence()

method

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

Value

An estimate of cell counts

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)
cellCounts <- estCellCounts.nPass(geneExpr=fullLM22, deconMatrices=deconMatrices, method='DCQ')

[Package ADAPTS version 1.0.6 Index]