fitPoisBG_sp | R Documentation |
Estimate Poisson background model for multiple slides:
fitPoisBG_sp(object, ...) ## S4 method for signature 'matrix' fitPoisBG_sp( object, id, iterations = 10, tol = 0.001, size_scale = c("sum", "first") )
object |
count matrix with features in rows and samples in columns |
... |
additional argument list that might be used |
id |
character vector same size as sample size representing slide names of each sample |
iterations |
maximum iterations to be run, default=10 |
tol |
tolerance to determine convergence, default = 1e-3 |
size_scale |
method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first" |
a list of following items
sizefact - estimated size factor
featfact - estimated feature factor matrix, column names the same as the slide id
countmat - the input count matrix
id - the input id
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