findOverlaps-methods: Find overlapping ranges for ChromatinAssay objects

Description Usage Arguments Details Value Functions See Also

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

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## 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

See Also


timoast/signac documentation built on Dec. 14, 2021, 11:34 p.m.