collapseCellTypes {ADAPTS}

Collapse cell types

Description

Collapse the cell types (in rows) to super-classes Including MGSM36 cell types

Usage

collapseCellTypes(cellCounts, method = "Pheno4")

Arguments

cellCounts

A matrix with cell counts

method

The method for combining cell types ('Default: 'Pheno2') Pheno1: Original cell-type based combinations Pheno2: Original cell-type based combinations, omitting Macrophages Pheno3: Alt Phenotype definitions based on WMB deconvolution correlations Pheno4: Consensus cell types Pheno5: Consensus cell types, combined myeloma & plasma Spillover1: Empirical combinations based on compToLM22source Spillover2: More agressive combination based on empirical combinations based on compToLM22source Spillover3: Combinations determined by spillToConvergence on 36 cell types

Value

a cell estimate matrix with the names changed

Examples

#This toy example 
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,] 

cellEst <- estCellPercent.DCQ(refExpr=smallLM22, geneExpr=fullLM22)
collapseCounts <- collapseCellTypes(cellCounts=cellEst)