iDEAWeight.fit | R Documentation |
Integrative DE and GSEA into a unfied framwork. The parameters of the model were infered via EM-MCMC algorithm.
iDEAWeight.fit( object, weight = NULL, fit_noGS = FALSE, init_beta = NULL, init_tau = c(-2, 0.5), min_degene = 5, em_iter = 15, mcmc_iter = 1000, fit.tol = 1e-05, verbose = TRUE, ... )
object |
iDEA object |
weight |
The weight for each gene to construct the gene-gene interation |
fit_noGS |
Bool variable to indicate whether fitting the model without the annoation |
init_beta |
Initial value for gene effect size, beta |
init_tau |
Initial value for annotations, including the intercept |
min_degene |
The threshold for the number of detected DE genes. For some of extremely cases, the method does not work when the number of detected DE genes is 0. |
em_iter |
Maximum iteration for EM algorithm |
mcmc_iter |
Maximum iteration for MCMC algorithm |
fit.tol |
Tol for fitting the model |
verbose |
Print the progresses |
... |
Ignored |
Returns a iDEA object with EM-MCMC results stored in object@de.
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