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Access genomic ranges for GRangesAssay objects

Source: R/granges-methods.R
granges-methods.Rd

Methods for accessing GenomicRanges::GRanges() object information stored in a GRangesAssay object.

Usage

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

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

Arguments

x

A GRangesAssay object

use.names

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

use.mcols

Not supported for GRangesAssay objects

...

Additional arguments

Value

Returns a GenomicRanges::GRanges() object

Functions

  • granges(Seurat): method for Seurat objects

See also

Examples

granges(atac_small)
#> GRanges object with 100 ranges and 0 metadata columns:
#>         seqnames          ranges strand
#>            <Rle>       <IRanges>  <Rle>
#>     [1]     chr1      9772-10660      *
#>     [2]     chr1   180712-181178      *
#>     [3]     chr1   181200-181607      *
#>     [4]     chr1   191183-192084      *
#>     [5]     chr1   267576-268461      *
#>     ...      ...             ...    ...
#>    [96]     chr1 1291564-1292473      *
#>    [97]     chr1 1299784-1300670      *
#>    [98]     chr1 1301689-1302543      *
#>    [99]     chr1 1305198-1306109      *
#>   [100]     chr1 1307720-1308738      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths