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

In timoast/signac: Analysis of Single-Cell Chromatin Data

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 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

timoast/signac documentation built on Jan. 1, 2023, 7:39 a.m.