This function 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,
verbose = TRUE,
seed = 11
)Arguments
- srt_merge
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
Whether data normalization should be performed. Default is
TRUE.- normalization_method
The normalization method to be used. Possible values are
"LogNormalize","SCT", and"TFIDF". Default is"LogNormalize".- do_HVF_finding
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.- verbose
Whether to print the message. Default is
TRUE.- seed
An integer specifying the random seed for reproducibility. Default is
11.