Description Usage Arguments Value
This function calls the MIXnorm function to obtain MLE of the mixture model, then produces the normalized expression matrix.
1 2 3 4 5 6 7 | func_MIXnorm(
dat,
max_iter = 15,
tol = 0.01,
log_file = "MIXnorm.log",
appr = T
)
|
dat |
input raw read count matrix. dim of dat = J genes * I samples. |
max_iter |
maximum number of iterations for the nested EM algorithm default is 15, recommend range (10, 50). |
tol |
convergency criteria, default is 1e-2, recommend range (1e-5,1). |
log_file |
file name that records the log. Default log file name is MIXnorm.log. |
appr |
binary True of False, indicates if the approximate version of normalization should be used. |
A list contains the normalized expression matrix, proportion of expressed genes and probabilities of being expressed for all genes.
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