Find overlapping ranges for ChromatinAssay objects

Source: R/iranges-methods.R

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

# 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
)

Arguments

query, subject

A ChromatinAssay object
maxgap, minoverlap, type, select, ignore.strand

See ?findOverlaps in the GenomicRanges and IRanges packages.

Value

See findOverlaps

Details

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

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

See also