Identify mitochondrial variants
Identify mitochondrial variants present in single cells.
IdentifyVariants(object, ...) ## Default S3 method: IdentifyVariants( object, refallele, stabilize_variance = TRUE, low_coverage_threshold = 10, verbose = TRUE, ... ) ## S3 method for class 'Assay' IdentifyVariants(object, refallele, ...) ## S3 method for class 'Seurat' IdentifyVariants(object, refallele, assay = NULL, ...)
object |
A Seurat object |
... |
Arguments passed to other methods |
refallele |
A dataframe containing reference alleles for the mitochondrial genome. |
stabilize_variance |
Stabilize variance |
low_coverage_threshold |
Low coverage threshold |
verbose |
Display messages |
assay |
Name of assay to use. If NULL, use the default assay. |
Returns a dataframe
## Not run: data.dir <- "path/to/data/directory" mgatk <- ReadMGATK(dir = data.dir) variant.df <- IdentifyVariants( object = mgatk$counts, refallele = mgatk$refallele ) ## End(Not run)
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