seqinfo-methods function

Access and modify sequence information for ChromatinAssay objects

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

## S4 replacement method for signature '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