findOverlaps-methods function

Find overlapping ranges for ChromatinAssay objects

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 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.

Returns

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

• findOverlaps-methods in the IRanges package.

• findOverlaps-methods in the GenomicRanges

  package

• ChromatinAssay-class