ADAPTS (version 1.0.22)

buildSpilloverMat: Build a spillover matrix

Description

Build a spillover matrix, i.e. what do purified samples deconvolve as?

spillExpr <- buildSpilloverMat(refExpr, geneExpr, method='DCQ')

Usage

buildSpilloverMat(refExpr, geneExpr, method = "DCQ")

Value

A spillover matrix showing how purified cell types deconvolve

Arguments

refExpr

The deconvolution matrix, e.g. LM22 or MGSM27

geneExpr

The full gene expression for purified cell types. Multiple columns (examples) for each column in the reference expr.

method

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

Examples

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

spillover <- buildSpilloverMat(refExpr=smallLM22, geneExpr=fullLM22, method='DCQ')