Access and modify sequence information for ChromatinAssay objects

Source: R/genomeinfodb-methods.R

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

# S4 method for class 'ChromatinAssay'
seqinfo(x)

# S4 method for class 'ChromatinAssay'
seqinfo(x) <- value

# S4 method for class 'ChromatinAssay'
seqlevels(x)

# S4 method for class 'ChromatinAssay'
seqlevels(x) <- value

# S4 method for class 'ChromatinAssay'
seqnames(x)

# S4 method for class 'ChromatinAssay'
seqnames(x) <- value

# S4 method for class 'ChromatinAssay'
seqlengths(x)

# S4 method for class 'ChromatinAssay'
seqlengths(x) <- value

# S4 method for class 'ChromatinAssay'
genome(x)

# S4 method for class 'ChromatinAssay'
genome(x) <- value

# S4 method for class 'ChromatinAssay'
isCircular(x)

# S4 method for class 'ChromatinAssay'
isCircular(x) <- value

# S4 method for class 'Seurat'
seqinfo(x)

# S4 method for class 'Seurat'
seqinfo(x) <- value

# S4 method for class 'Seurat'
seqlevels(x)

# S4 method for class 'Seurat'
seqlevels(x) <- value

# S4 method for class 'Seurat'
seqnames(x)

# S4 method for class 'Seurat'
seqnames(x) <- value

# S4 method for class 'Seurat'
seqlengths(x)

# S4 method for class 'Seurat'
seqlengths(x) <- value

# S4 method for class 'Seurat'
genome(x)

# S4 method for class 'Seurat'
genome(x) <- value

# S4 method for class 'Seurat'
isCircular(x)

# S4 method for class '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