Check and preprocess a list of Seurat objects

Checks and preprocesses a list of Seurat objects. It performs various checks on the input, including verification of input types, assay type consistency, feature name consistency, and batch column consistency. It also performs data normalization and variable feature finding based on the specified parameters. Finally, it prepares the data for integration analysis based on the highly variable features.

Usage

CheckDataList(
  srt_list,
  batch,
  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_list: A list of Seurat objects to be checked and preprocessed.
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.

Value

A list containing the preprocessed Seurat objects, the highly variable features, the assay name, and the type of assay.