Description Usage Arguments Value Examples
Generates factorized matrices showing the contribution of each feature in each cell population or each cell population in each sample.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  factorizeMatrix(x, celdaMod, ...)
## S4 method for signature 'SingleCellExperiment,ANY'
factorizeMatrix(
x,
useAssay = "counts",
altExpName = "featureSubset",
type = c("counts", "proportion", "posterior")
)
## S4 method for signature 'matrix,celda_CG'
factorizeMatrix(x, celdaMod, type = c("counts", "proportion", "posterior"))
## S4 method for signature 'matrix,celda_C'
factorizeMatrix(x, celdaMod, type = c("counts", "proportion", "posterior"))
## S4 method for signature 'matrix,celda_G'
factorizeMatrix(x, celdaMod, type = c("counts", "proportion", "posterior"))

x 
Can be one of

celdaMod 
Celda model object. Only works if 
... 
Ignored. Placeholder to prevent check warning. 
useAssay 
A string specifying which assay
slot to use if 
altExpName 
The name for the altExp slot to use. Default "featureSubset". 
type 
Character vector. A vector containing one or more of "counts",
"proportion", or "posterior". "counts" returns the raw number of counts for
each factorized matrix. "proportions" returns the normalized probabilities
for each factorized matrix, which are calculated by dividing the raw counts
in each factorized matrix by the total counts in each column. "posterior"
returns the posterior estimates which include the addition of the Dirichlet
concentration parameter (essentially as a pseudocount). Default

For celda_CG model, A list with elements for "counts", "proportions", or "posterior" probabilities. Each element will be a list containing factorized matrices for "module", "cellPopulation", and "sample". Additionally, the contribution of each module in each individual cell will be included in the "cell" element of "counts" and "proportions" elements.
For celda_C model, a list with elements for "counts", "proportions", or "posterior" probabilities. Each element will be a list containing factorized matrices for "module" and "sample".
For celda_G model, a list with elements for "counts", "proportions", or "posterior" probabilities. Each element will be a list containing factorized matrices for "module" and "cell".
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  data(sceCeldaCG)
factorizedMatrices < factorizeMatrix(sceCeldaCG, type = "posterior")
data(celdaCGSim, celdaCGMod)
factorizedMatrices < factorizeMatrix(
celdaCGSim$counts,
celdaCGMod,
"posterior")
data(celdaCSim, celdaCMod)
factorizedMatrices < factorizeMatrix(
celdaCSim$counts,
celdaCMod, "posterior"
)
data(celdaGSim, celdaGMod)
factorizedMatrices < factorizeMatrix(
celdaGSim$counts,
celdaGMod, "posterior"
)

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