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

seqinfo-methodsR Documentation

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-method: set method for ChromatinAssay objects

  • seqlevels,ChromatinAssay-method: get method for ChromatinAssay objects

  • seqlevels<-,ChromatinAssay-method: set method for ChromatinAssay objects

  • seqnames,ChromatinAssay-method: get method for ChromatinAssay objects

  • seqnames<-,ChromatinAssay-method: set method for ChromatinAssay objects

  • seqlengths,ChromatinAssay-method: get method for ChromatinAssay objects

  • seqlengths<-,ChromatinAssay-method: set method for ChromatinAssay objects

  • genome,ChromatinAssay-method: get method for ChromatinAssay objects

  • genome<-,ChromatinAssay-method: set method for ChromatinAssay objects

  • isCircular,ChromatinAssay-method: get method for ChromatinAssay objects

  • isCircular<-,ChromatinAssay-method: set method for ChromatinAssay objects

  • seqinfo,Seurat-method: get method for Seurat objects

  • seqinfo<-,Seurat-method: set method for Seurat objects

  • seqlevels,Seurat-method: get method for Seurat objects

  • seqlevels<-,Seurat-method: set method for Seurat objects

  • seqnames,Seurat-method: get method for Seurat objects

  • seqnames<-,Seurat-method: set method for Seurat objects

  • seqlengths,Seurat-method: get method for Seurat objects

  • seqlengths<-,Seurat-method: set method for Seurat objects

  • genome,Seurat-method: get method for Seurat objects

  • genome<-,Seurat-method: set method for Seurat objects

  • isCircular,Seurat-method: get method for Seurat objects

  • isCircular<-,Seurat-method: set method for Seurat objects

See Also

  • seqinfo in the GenomeInfoDb package.

  • ChromatinAssay-class


timoast/signac documentation built on April 2, 2022, 2:19 a.m.