Signac: findOverlaps-methods – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

findOverlaps-methods

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,ChromatinAssay,Vector-method: method for ChromatinAssay, Vector
findOverlaps,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
findOverlaps,Vector,Seurat-method: method for Vector, Seurat
findOverlaps,Seurat,Vector-method: method for Seurat, Vector
findOverlaps,Seurat,Seurat-method: method for Seurat, Seurat
countOverlaps,Vector,ChromatinAssay-method: method for Vector, ChromatinAssay
countOverlaps,ChromatinAssay,Vector-method: method for ChromatinAssay, Vector
countOverlaps,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
countOverlaps,Seurat,Vector-method: method for Seurat, Vector
countOverlaps,Vector,Seurat-method: method for Vector, Seurat
countOverlaps,Seurat,Seurat-method: method for Seurat, Seurat