runLiger_online_iNMF: Run runLiger_online_iNMF integration (see also...

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Run runLiger_online_iNMF integration (see also http://htmlpreview.github.io/?https://github.com/welch-lab/liger/blob/master/vignettes/online_iNMF_tutorial.html)

Description

Run runLiger_online_iNMF integration (see also http://htmlpreview.github.io/?https://github.com/welch-lab/liger/blob/master/vignettes/online_iNMF_tutorial.html)

Usage

runLiger_online_iNMF(
  object,
  liger.k = 30,
  liger.miniBatch_size = 5000,
  liger.max.epochs = 5
)

Arguments

object	The SingCellaR object.
liger.k	Inner dimension of factorization–number of metagenes (default 30). A value in the range 20-50 works well for most analyses.
liger.miniBatch_size	Total number of cells in each minibatch (default 5000). This is a reasonable default, but a smaller value such as 1000 may be necessary for analyzing very small datasets. In general, minibatch size should be no larger than the number of cells in the smallest dataset.
liger.max.epochs	Maximum number of epochs (complete passes through the data). (default 5)

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.