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 class '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 class '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 class '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 class '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 class '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 class '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 class 'Vector,ChromatinAssay'
countOverlaps(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ignore.strand = FALSE
)

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

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

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

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

# S4 method for class '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(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