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Signac (version 1.14.0)

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

Value

See findOverlaps

Arguments

query, subject

A ChromatinAssay object

maxgap, minoverlap, type, select, ignore.strand

See ?findOverlaps in the GenomicRanges and IRanges packages.

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

Details

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

See Also

  • findOverlaps-methods in the IRanges package.

  • findOverlaps-methods in the GenomicRanges package

  • ChromatinAssay-class