rliger-deprecated: Deprecated functions in package 'rliger'.

In rliger: Linked Inference of Genomic Experimental Relationships

Deprecated functions in package rliger.

Description

The functions listed below are deprecated and will be defunct in the near future. When possible, alternative functions with similar functionality or a replacement are also mentioned. Help pages for deprecated functions are available at help("<function>-deprecated").

Usage

makeInteractTrack(
  corr.mat,
  path_to_coords,
  genes.list = NULL,
  output_path = getwd()
)

louvainCluster(
  object,
  resolution = 1,
  k = 20,
  prune = 1/15,
  eps = 0.1,
  nRandomStarts = 10,
  nIterations = 100,
  random.seed = 1,
  verbose = getOption("ligerVerbose", TRUE),
  dims.use = NULL
)

optimizeALS(
  object,
  k,
  lambda = 5,
  thresh = NULL,
  max.iters = 30,
  nrep = 1,
  H.init = NULL,
  W.init = NULL,
  V.init = NULL,
  use.unshared = FALSE,
  rand.seed = 1,
  print.obj = NULL,
  verbose = TRUE,
  ...
)

online_iNMF(
  object,
  X_new = NULL,
  projection = FALSE,
  W.init = NULL,
  V.init = NULL,
  H.init = NULL,
  A.init = NULL,
  B.init = NULL,
  k = 20,
  lambda = 5,
  max.epochs = 5,
  miniBatch_max_iters = 1,
  miniBatch_size = 5000,
  h5_chunk_size = 1000,
  seed = 123,
  verbose = TRUE
)

quantile_norm(
  object,
  quantiles = 50,
  ref_dataset = NULL,
  min_cells = 20,
  knn_k = 20,
  dims.use = NULL,
  do.center = FALSE,
  max_sample = 1000,
  eps = 0.9,
  refine.knn = TRUE,
  clusterName = "H.norm_cluster",
  rand.seed = 1,
  verbose = getOption("ligerVerbose", TRUE)
)

makeRiverplot(
  object,
  cluster1,
  cluster2,
  cluster_consensus = NULL,
  min.frac = 0.05,
  min.cells = 10,
  river.yscale = 1,
  river.lty = 0,
  river.node_margin = 0.1,
  label.cex = 1,
  label.col = "black",
  lab.srt = 0,
  river.usr = NULL,
  node.order = "auto"
)

makeInteractTrack

For makeInteractTrack, use exportInteractTrack.

louvainCluster

For louvainCluster, use runCluster(method = "louvain") as the replacement, while runCluster with default method = "leiden" is more recommended.

optimizeALS

For optimizeALS, use runIntegration or runINMF. For the case of optimizeALS(use.unshared = TRUE), use runIntegration with method = "UINMF" or runUINMF instead.

online_iNMF

For online_iNMF, use runIntegration with method = "online" or runOnlineINMF.

quantile_norm

For quantile_norm, use quantileNorm.

makeRiverplot

For makeRiverplot, use plotSankey as the replacement.

rliger documentation built on Aug. 27, 2025, 1:08 a.m.