This function checks and preprocesses a merged seurat object.
Usage
check_srtMerge(
srtMerge,
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,
seed = 11,
check_v5 = TRUE
)Arguments
- srtMerge
A merged Seurat object that includes the batch information.
- 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.