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][GenomicRanges::findOverlaps]⁠ in the GenomicRanges and IRanges packages.

Details

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

Value

See GenomicRanges::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

Signac documentation built on April 1, 2026, 5:06 p.m.