View source: R/onlyDeconAlgorithms.R
buildSpilloverMat | R Documentation |
Build a spillover matrix, i.e. what do purified samples deconvolve as?
spillExpr <- buildSpilloverMat(refExpr, geneExpr, method='DCQ')
buildSpilloverMat(refExpr, geneExpr, method = "DCQ")
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) |
A spillover matrix showing how purified cell types deconvolve
#This toy example library(ADAPTS) fullLM22 <- ADAPTS::LM22[1:30, 1:4] smallLM22 <- fullLM22[1:25,] spillover <- buildSpilloverMat(refExpr=smallLM22, geneExpr=fullLM22, method='DCQ')
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