
Compute the GC content, region lengths, and dinucleotide base frequencies for regions in the assay and add to the feature metadata.
RegionStats(object, ...)# S3 method for default
RegionStats(object, genome, sep = c("-", "-"), verbose = TRUE, ...)
# S3 method for Assay
RegionStats(object, genome, sep = c("-", "-"), verbose = TRUE, ...)
# S3 method for Seurat
RegionStats(
object,
genome,
assay = NULL,
sep = c("-", "-"),
verbose = TRUE,
...
)
A Seurat object, Assay object, or set of genomic ranges
Arguments passed to other methods
A BSgenome object
A length-2 character vector containing the separators to be used when constructing genomic coordinates from the regions. The first element is used to separate the chromosome from the genomic coordinates, and the second element used to separate the start and end coordinates.
Display messages
Name of assay to use
Returns a dataframe
# NOT RUN {
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
object = rownames(atac_small),
genome = BSgenome.Hsapiens.UCSC.hg19, sep = c(":", "-")
)
# }
# NOT RUN {
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
object = atac_small[['peaks']],
genome = BSgenome.Hsapiens.UCSC.hg19, sep = c(":", "-")
)
# }
# NOT RUN {
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
object = atac_small,
assay = 'bins',
genome = BSgenome.Hsapiens.UCSC.hg19
)
# }
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