RunjrSiCKLSNMF: Run jrSiCKLSNMF on an object of class SickleJr

In jrSiCKLSNMF: Multimodal Single-Cell Omics Dimensionality Reduction

Run jrSiCKLSNMF on an object of class SickleJr

Description

Wrapper function to run jrSiCKLSNMF on an object of class SickleJr. Performs jrSiCKLSNMF on the given SickleJr

Usage

RunjrSiCKLSNMF(
  SickleJr,
  rounds = 30000,
  differr = 1e-06,
  display_progress = TRUE,
  lossonsubset = FALSE,
  losssubsetsize = dim(SickleJr@H)[1],
  minibatch = FALSE,
  batchsize = 1000,
  random_W_updates = FALSE,
  seed = NULL,
  minrounds = 200,
  suppress_warnings = FALSE,
  subsample = 1:dim([e-mail][[1]])[2]
)

Arguments

SickleJr	An object of class SickleJr
rounds	Number of rounds: defaults to 2000
differr	Tolerance for percentage change in loss between updates: defaults to 1e-6
display_progress	Boolean indicating whether to display the progress bar for jrSiCKLSNMF
lossonsubset	Boolean indicating whether to use a subset to calculate the loss function rather than the whole dataset
losssubsetsize	Size of the subset of data on which to calculate the loss
minibatch	Boolean indicating whether to use mini-batch updates
batchsize	Size of batch for mini-batch updates
random_W_updates	Boolean indicating whether or not to use random_W_updates updates (i.e. only update \mathbf{W}^v once per mini-batch epoch)
seed	Number specifying desired random seed
minrounds	Minimum number of rounds: most helpful for the mini-batch algorithm
suppress_warnings	Boolean indicating whether to suppress warnings
subsample	A numeric used primarily when finding an appropriate number of latent factors: defaults to total number of cells

Value

An object of class SickleJr with updated \mathbf{W}^v matrices, updated \mathbf{H} matrix, and a vector of values for the loss function added to the Wlist, H, and loss slots, respectively

References

\insertRef

Cai2008jrSiCKLSNMF

\insertRef

jnmf2009jrSiCKLSNMF

\insertRef

Eddelbuettel2011jrSiCKLSNMF

\insertRef

Eddelbuettel2014jrSiCKLSNMF

\insertRef

Elyanow2020jrSiCKLSNMF

\insertRef

halfbakednmfjrSiCKLSNMF

\insertRef

Lee1999jrSiCKLSNMF

\insertRef

Liu2013jrSiCKLSNMF

Examples

SimSickleJrSmall<-RunjrSiCKLSNMF(SimSickleJrSmall,rounds=5)

jrSiCKLSNMF documentation built on Aug. 12, 2025, 1:08 a.m.