ScVI integration function

Usage

scVI_integrate(
  srt_merge = NULL,
  batch = NULL,
  append = TRUE,
  srt_list = NULL,
  assay = NULL,
  do_normalization = NULL,
  normalization_method = "LogNormalize",
  do_HVF_finding = TRUE,
  HVF_source = "separate",
  HVF_method = "vst",
  nHVF = 2000,
  HVF_min_intersection = 1,
  HVF = NULL,
  scVI_dims_use = NULL,
  nonlinear_reduction = "umap",
  nonlinear_reduction_dims = c(2, 3),
  nonlinear_reduction_params = list(),
  force_nonlinear_reduction = TRUE,
  neighbor_metric = "euclidean",
  neighbor_k = 20L,
  cluster_algorithm = "louvain",
  cluster_resolution = 0.6,
  model = "SCVI",
  SCVI_params = list(),
  PEAKVI_params = list(),
  POISSONVI_params = list(),
  train_params = list(),
  cores = 1,
  verbose = TRUE,
  seed = 11
)

Arguments

srt_merge: A merged `Seurat` object that includes the batch information.
batch: Batch variable name.
append: Append integrated results to srt_merge.
srt_list: A list of Seurat objects to be checked and preprocessed.
assay: Assay to use. NULL uses the default assay.
do_normalization: Whether data normalization should be performed.
normalization_method: The normalization method to be used. Possible values are "LogNormalize", "SCT", "TFIDF", and "scran".
do_HVF_finding, HVF_method, nHVF, HVF: Highly variable features. HVF_method is "vst", "mvp", "disp", or "scran".
HVF_source: The source of highly variable features. Possible values are "global" and "separate".
HVF_min_intersection: The feature needs to be present in batches for a minimum number of times in order to be considered as highly variable.
scVI_dims_use: Dimensions returned by scVI that will be utilized for downstream cell cluster finding and nonlinear reduction. If set to NULL, all the returned dimensions will be used by default.
nonlinear_reduction, nonlinear_reduction_dims, nonlinear_reduction_params, force_nonlinear_reduction: Nonlinear reduction ("umap", "umap-naive", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr").
neighbor_metric, neighbor_k: Neighbor graph ("euclidean", "cosine", "manhattan", "hamming").
cluster_algorithm, cluster_resolution: Clustering ("louvain", "slm", "leiden"). Larger cluster_resolution yields fewer clusters.
model: A string indicating the scVI model to be used. Options are "SCVI", "PEAKVI", and "POISSONVI".
SCVI_params: A list of parameters for the SCVI model.
PEAKVI_params: A list of parameters for the PEAKVI model.
POISSONVI_params: A list of parameters for the POISSONVI model.
train_params: A list of parameters passed to the model `train()` method.
cores: An integer setting the number of threads for `scVI`.
verbose: Whether to print the message. Default is TRUE.
seed: Random seed.

Examples

if (FALSE) { # \dontrun{
data("pbmcmultiome_sub", package = "scop")
pbmcmultiome_sub$batch <- rep(c("batch1", "batch2"), length.out = ncol(pbmcmultiome_sub))
pbmcmultiome_sub <- scVI_integrate(
  srt_merge = pbmcmultiome_sub,
  batch = "batch",
  assay = "peaks",
  model = "PEAKVI",
  train_params = list(max_epochs = 2L)
)
pbmcmultiome_sub <- scVI_integrate(
  srt_merge = pbmcmultiome_sub,
  batch = "batch",
  assay = "peaks",
  model = "POISSONVI",
  train_params = list(max_epochs = 2L)
)
} # }