View source: R/onlyDeconAlgorithms.R
spillToConvergence | R Documentation |
Build an n-pass spillover matrix, continuing until the results converge into clusters of cell types
deconMatrices <- spillToConvergence(sigMatrix, geneExpr, 100, FALSE, TRUE)
spillToConvergence( sigMatrix, geneExpr, nPasses = 100, plotIt = FALSE, imputNAs = FALSE, 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 (DEFAULT: 100) |
plotIt |
Set to TRUE to plot it (DEFAULT: FALSE) |
imputNAs |
Set to TRUE to imput genes with missing values & cache the imputed. FALSE will just remove them (DEFAULT: FALSE) |
method |
One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ) |
A list of signature matrices
#This toy example library(ADAPTS) fullLM22 <- ADAPTS::LM22[1:30, 1:4] smallLM22 <- fullLM22[1:25,] deconMatrices <- spillToConvergence(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10, plotIt=TRUE)
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