Access genomic ranges for ChromatinAssay objects

Methods for accessing GRanges object information stored in a ChromatinAssay object.

# S4 method for ChromatinAssay
granges(x, use.names = TRUE, use.mcols = FALSE, ...)

# S4 method for Seurat
granges(x, use.names = TRUE, use.mcols = FALSE, ...)

Arguments

x

A ChromatinAssay object

use.names

Whether the names on the genomic ranges should be propagated to the returned object.

use.mcols

Not supported for ChromatinAssay objects

...

Additional arguments

Value

Returns a GRanges object

Functions

• granges(Seurat): method for Seurat objects

See also

• granges in the GenomicRanges package.

• ChromatinAssay-class

Examples

granges(atac_small)
#> GRanges object with 323 ranges and 0 metadata columns:
#>         seqnames          ranges strand
#>            <Rle>       <IRanges>  <Rle>
#>     [1]     chr1   713460-714823      *
#>     [2]     chr1   752422-753038      *
#>     [3]     chr1   762106-763359      *
#>     [4]     chr1   779589-780271      *
#>     [5]     chr1   804872-805761      *
#>     ...      ...             ...    ...
#>   [319]     chr1 9299648-9300348      *
#>   [320]     chr1 9327071-9327557      *
#>   [321]     chr1 9335457-9336176      *
#>   [322]     chr1 9349019-9350779      *
#>   [323]     chr1 9352328-9354391      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths