Check and preprocess a merged seurat object

Checks and preprocesses a merged seurat object.

Usage

CheckDataMerge(
  srt_merge,
  batch = 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,
  vars_to_regress = NULL,
  cores = 1L,
  verbose = TRUE,
  seed = 11
)

Arguments

srt_merge: A merged `Seurat` object that includes the batch information.
batch: Batch variable name.
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.
vars_to_regress: A vector of variable names to include as additional regression variables.
cores: Number of CPU cores.
verbose: Whether to print the message. Default is TRUE.
seed: Random seed.

Check and preprocess a merged seurat object

Usage

Arguments

See also