para_est_new {scpoisson} | R Documentation |
Parameter estimates based on two-way approximation
Description
This function returns a vector consists of parameter estimates for overall offset, cell effect, and gene effect.
Usage
para_est_new(test_set)
Arguments
test_set |
A UMI count data matrix with genes as rows and cells as columns |
Details
This is a function used to calculate parameter estimates based on
\lambda_{gc} = e^{\mu + \alpha_g + \beta_c}
,
where \mu
is the overall offset,
\alpha
is a vector with the same length as the number of genes,
and \beta
is a vector with the same length as the number of cells.
The order of elements in vectors \alpha
or \beta
is the same as rows (genes) or
cells (columns) from input data. Be sure to remove cells/genes with all zeros.
Value
A numeric vector containing parameter estimates from overall offset (first element), gene effect (same order as rows) and cell effect (same order as columns).
Examples
# Matrix as input
test_set <- matrix(rpois(500, 0.5), nrow = 10)
para_est_new(test_set)