This function 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
check_srtList(
srtList,
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,
seed = 11
)Arguments
- srtList
A list of Seurat objects to be checked and preprocessed.
- batch
A character string specifying the batch variable name.
- assay
The name of the assay to be used for downstream analysis.
- do_normalization
A logical value indicating whether data normalization should be performed.
- normalization_method
The normalization method to be used. Possible values are "LogNormalize", "SCT", and "TFIDF". Default is "LogNormalize".
- do_HVF_finding
A logical value indicating whether highly variable feature (HVF) finding should be performed. Default is TRUE.
- HVF_source
The source of highly variable features. Possible values are "global" and "separate". Default is "separate".
- HVF_method
The method for selecting highly variable features. Default is "vst".
- nHVF
The number of highly variable features to select. Default is 2000.
- 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. The default value is 1.
- HVF
A vector of highly variable features. Default is NULL.
- vars_to_regress
A vector of variable names to include as additional regression variables. Default is NULL.
- seed
An integer specifying the random seed for reproducibility. Default is 11.