estCellCounts.nPass: Deconvolve with an n-pass spillover matrix
In yxinyi2/ADAPTS1.0.3: Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells
Description
Usage
Arguments
Value
Examples
View source: R/onlyDeconAlgorithms.R
Description
curExpr <- estCellCounts.nPass(sigMatrix, deconMatrices)
Usage
1
estCellCounts.nPass(geneExpr, deconMatrices, method = "DCQ")
Arguments
geneExpr
The gene expression matrix
deconMatrices
The results from spillToConvergence()
method
One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ)
Value
An estimate of cell counts
Examples
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#This toy example
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,]
deconMatrices <- spillToConvergence(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10)
cellCounts <- estCellCounts.nPass(geneExpr=fullLM22, deconMatrices=deconMatrices, method='DCQ')
yxinyi2/ADAPTS1.0.3 documentation built on Aug. 5, 2020, 12:09 a.m.
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Description Usage Arguments Value Examples
View source: R/onlyDeconAlgorithms.R
Description
curExpr <- estCellCounts.nPass(sigMatrix, deconMatrices)
Usage
1 | estCellCounts.nPass(geneExpr, deconMatrices, method = "DCQ")
|
Arguments
geneExpr |
The gene expression matrix |
deconMatrices |
The results from spillToConvergence() |
method |
One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ) |
Value
An estimate of cell counts
Examples
1 2 3 4 5 6 7 | #This toy example
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,]
deconMatrices <- spillToConvergence(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10)
cellCounts <- estCellCounts.nPass(geneExpr=fullLM22, deconMatrices=deconMatrices, method='DCQ')
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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