findOverlaps-methods: Find overlapping ranges for ChromatinAssay objects

In Signac: Analysis of Single-Cell Chromatin Data

Find overlapping ranges for ChromatinAssay objects

Description

The findOverlaps, countOverlaps methods are available for ChromatinAssay objects. This allows finding overlaps between genomic ranges and the ranges stored in the ChromatinAssay.

Usage

## S4 method for signature 'Vector,ChromatinAssay'
findOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  select = c("all", "first", "last", "arbitrary"),
  ignore.strand = FALSE
)

## S4 method for signature 'ChromatinAssay,Vector'
findOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  select = c("all", "first", "last", "arbitrary"),
  ignore.strand = FALSE
)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
findOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  select = c("all", "first", "last", "arbitrary"),
  ignore.strand = FALSE
)

## S4 method for signature 'Vector,Seurat'
findOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  select = c("all", "first", "last", "arbitrary"),
  ignore.strand = FALSE
)

## S4 method for signature 'Seurat,Vector'
findOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  select = c("all", "first", "last", "arbitrary"),
  ignore.strand = FALSE
)

## S4 method for signature 'Seurat,Seurat'
findOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  select = c("all", "first", "last", "arbitrary"),
  ignore.strand = FALSE
)

## S4 method for signature 'Vector,ChromatinAssay'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

## S4 method for signature 'ChromatinAssay,Vector'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

## S4 method for signature 'Seurat,Vector'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

## S4 method for signature 'Vector,Seurat'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

## S4 method for signature 'Seurat,Seurat'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

Arguments

query, subject	A ChromatinAssay object
maxgap, minoverlap, type, select, ignore.strand	See ?findOverlaps in the GenomicRanges and IRanges packages.

Details

If a ChromatinAssay is set as the default assay in a Seurat object, you can also call findOverlaps directly on the Seurat object.

Value

See findOverlaps

Functions

• findOverlaps(query = ChromatinAssay, subject = Vector): method for ChromatinAssay, Vector

• findOverlaps(query = ChromatinAssay, subject = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• findOverlaps(query = Vector, subject = Seurat): method for Vector, Seurat

• findOverlaps(query = Seurat, subject = Vector): method for Seurat, Vector

• findOverlaps(query = Seurat, subject = Seurat): method for Seurat, Seurat

• countOverlaps(query = Vector, subject = ChromatinAssay): method for Vector, ChromatinAssay

• countOverlaps(query = ChromatinAssay, subject = Vector): method for ChromatinAssay, Vector

• countOverlaps(query = ChromatinAssay, subject = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• countOverlaps(query = Seurat, subject = Vector): method for Seurat, Vector

• countOverlaps(query = Vector, subject = Seurat): method for Vector, Seurat

• countOverlaps(query = Seurat, subject = Seurat): method for Seurat, Seurat

See Also

• findOverlaps-methods in the IRanges package.

• findOverlaps-methods in the GenomicRanges package

• ChromatinAssay-class

Signac documentation built on Sept. 11, 2024, 9:30 p.m.