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Signac (version 1.14.0)

seqinfo-methods: Access and modify sequence information for ChromatinAssay objects

Description

Methods for accessing and modifying Seqinfo object information stored in a ChromatinAssay object.

Usage

# S4 method for ChromatinAssay
seqinfo(x)
# S4 method for ChromatinAssay
seqinfo(x) <- value
# S4 method for ChromatinAssay
seqlevels(x)
# S4 method for ChromatinAssay
seqlevels(x) <- value
# S4 method for ChromatinAssay
seqnames(x)
# S4 method for ChromatinAssay
seqnames(x) <- value
# S4 method for ChromatinAssay
seqlengths(x)
# S4 method for ChromatinAssay
seqlengths(x) <- value
# S4 method for ChromatinAssay
genome(x)
# S4 method for ChromatinAssay
genome(x) <- value
# S4 method for ChromatinAssay
isCircular(x)
# S4 method for ChromatinAssay
isCircular(x) <- value
# S4 method for Seurat
seqinfo(x)
# S4 method for Seurat
seqinfo(x) <- value
# S4 method for Seurat
seqlevels(x)
# S4 method for Seurat
seqlevels(x) <- value
# S4 method for Seurat
seqnames(x)
# S4 method for Seurat
seqnames(x) <- value
# S4 method for Seurat
seqlengths(x)
# S4 method for Seurat
seqlengths(x) <- value
# S4 method for Seurat
genome(x)
# S4 method for Seurat
genome(x) <- value
# S4 method for Seurat
isCircular(x)
# S4 method for Seurat
isCircular(x) <- value

Arguments

x

A ChromatinAssay object

value

A Seqinfo object or name of a UCSC genome to store in the ChromatinAssay

Functions

  • seqinfo(ChromatinAssay) <- value: set method for ChromatinAssay objects

  • seqlevels(ChromatinAssay): get method for ChromatinAssay objects

  • seqlevels(ChromatinAssay) <- value: set method for ChromatinAssay objects

  • seqnames(ChromatinAssay): get method for ChromatinAssay objects

  • seqnames(ChromatinAssay) <- value: set method for ChromatinAssay objects

  • seqlengths(ChromatinAssay): get method for ChromatinAssay objects

  • seqlengths(ChromatinAssay) <- value: set method for ChromatinAssay objects

  • genome(ChromatinAssay): get method for ChromatinAssay objects

  • genome(ChromatinAssay) <- value: set method for ChromatinAssay objects

  • isCircular(ChromatinAssay): get method for ChromatinAssay objects

  • isCircular(ChromatinAssay) <- value: set method for ChromatinAssay objects

  • seqinfo(Seurat): get method for Seurat objects

  • seqinfo(Seurat) <- value: set method for Seurat objects

  • seqlevels(Seurat): get method for Seurat objects

  • seqlevels(Seurat) <- value: set method for Seurat objects

  • seqnames(Seurat): get method for Seurat objects

  • seqnames(Seurat) <- value: set method for Seurat objects

  • seqlengths(Seurat): get method for Seurat objects

  • seqlengths(Seurat) <- value: set method for Seurat objects

  • genome(Seurat): get method for Seurat objects

  • genome(Seurat) <- value: set method for Seurat objects

  • isCircular(Seurat): get method for Seurat objects

  • isCircular(Seurat) <- value: set method for Seurat objects

See Also

  • seqinfo in the GenomeInfoDb package.

  • ChromatinAssay-class