Select the parameters in COAP models

Select the number of factors and the rank of coefficient matrix in the covariate-augmented overdispersed Poisson factor model

selectParams(
  X_count,
  Z,
  multiFac = rep(1, nrow(X_count)),
  q_max = 15,
  r_max = 24,
  threshold = c(0.1, 0.01),
  verbose = TRUE,
  ...
)

Arguments

X_count: a count matrix, the observed count matrix.
Z: an optional matrix, the covariate matrix; default as a full-one column vector if there is no additional covariates.
multiFac: an optional vector, the normalization factor for each unit; default as full-one vector.
q_max: an optional string, specify the upper bound for the number of factors; default as 15.
r_max: an optional integer, specify the upper bound for the rank of the regression coefficient matrix; default as 24.
threshold: an optional 2-dimensional positive vector, specify the the thresholds that filters the singular values of beta and B, respectively.
verbose: a logical value, whether output the information in iteration.
maxIter: the maximum iteration of the VEM algorithm. The default is 30.
joint_opt_beta: a logical value, whether use the joint optimization method to update bbeta. The default is FALSE, which means using the separate optimization method.
fast_svd: a logical value, whether use the fast SVD algorithm in the update of bbeta; default is TRUE.

return a named vector with names `hr` and `hq`, the estimated rank and number of factors.

The threshold is to filter the singular values with low signal, to assist the identification of underlying model structure.

None