run_scAI: run scAI model

In sqjin/scAI: integrative analysis of single-cell transcriptomic and epigenomic profiles

Description

run scAI model

Usage

run_scAI(
  object,
  K,
  do.fast = FALSE,
  nrun = 5L,
  hvg.use1 = FALSE,
  hvg.use2 = FALSE,
  keep_all = F,
  s = 0.25,
  alpha = 1,
  lambda = 1e+05,
  gamma = 1,
  maxIter = 500L,
  stop_rule = 1L,
  init = NULL,
  rand.seed = 1L
)

Arguments

object	scAI object
K	An integer indicating the Rank of the inferred factor
do.fast	whether use the python version for running scAI optimization model
nrun	Number of times to repreat the running
hvg.use1	whether use high variable genes for RNA-seq data
hvg.use2	whether use high variable genes for ATAC-seq data
keep_all	Whether keep all the results from multiple runs
s	Probability of Bernoulli distribution
alpha	model parameter
lambda	model parameter
gamma	model parameter
maxIter	An integer indicating Maximum number of iteration
stop_rule	Stop rule to be used
init	List of the initialized low-rank matrices
rand.seed	An integer indicating the seed

sqjin/scAI documentation built on Nov. 19, 2020, 4:04 p.m.