View source: R/onlyDeconAlgorithms.R
clustWspillOver | R Documentation |
Build clusters based on n-pass spillover matrix
clustWspillOver( sigMatrix, geneExpr, nPasses = 100, deconMatrices = NULL, method = "DCQ" )
sigMatrix |
The deconvolution matrix, e.g. LM22 or MGSM27 |
geneExpr |
The source gene expression matrix used to calculate sigMatrix. |
nPasses |
The maximum number of iterations for spillToConvergence (DEFAULT: 100) |
deconMatrices |
Optional pre-computed results from spillToConvergence (DEFAULT: NULL) |
method |
One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ) |
Cell types grouped by cluster
#This toy example library(ADAPTS) fullLM22 <- ADAPTS::LM22[1:30, 1:4] smallLM22 <- fullLM22[1:25,] clusters <- clustWspillOver(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10)
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