View source: R/data_processing.R
CleanCODEX.nb.internal | R Documentation |
Removes noise from CODEX protein data by fitting a two-component Negative Binomial mixture and computing each expression measurement as the cumulative distribution of the Negative Binomial with the higher median. Normalizes CODEX protein data by the original total counts per cell. Takes matrices and data frames instead of STvEA.data class
CleanCODEX.nb.internal(
codex_protein,
num_cores = 1,
maxit = 500,
factr = 1e-09,
optim_inits = NULL,
normalize = FALSE
)
codex_protein |
Raw CODEX protein data (cell x protein) |
num_cores |
number of cores to use for parallelized fits. On Windows, this must be set to 1. |
maxit |
maximum number of iterations for optim function |
factr |
accuracy of optim function |
optim_inits |
a matrix of (proteins x params) with initialization parameters for each protein to input to the optim function. If NULL, starts at two default parameter sets and picks the better one |
normalize |
divide cleaned CODEX expression by total expression per cell |
Cleaned CODEX protein data matrix (cell x protein)
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