buildSpilloverMat {ADAPTS}R Documentation

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")

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)

Value

A spillover matrix showing how purified cell types deconvolve

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')

[Package ADAPTS version 1.0.6 Index]