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Find overlapping ranges for GRangesAssay objects

Source: R/iranges-methods.R
findOverlaps-methods.Rd

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

Usage

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

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

# S4 method for class 'GRangesAssay,GRangesAssay'
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 GRangesAssay object

maxgap, minoverlap, type, select, ignore.strand

See ?[findOverlaps][GenomicRanges::findOverlaps] in the GenomicRanges::GenomicRanges and IRanges::IRanges packages.

Value

See GenomicRanges::findOverlaps()

Details

If a GRangesAssay assay is set as the default assay in a SeuratObject::Seurat() object, you can also call findOverlaps directly on the Seurat object.

Functions

  • findOverlaps(query = GRangesAssay, subject = Vector): method for GRangesAssay, Vector

  • findOverlaps(query = GRangesAssay, subject = GRangesAssay): method for GRangesAssay, GRangesAssay

  • 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 = GRangesAssay): method for Vector, GRangesAssay

  • countOverlaps(query = GRangesAssay, subject = Vector): method for GRangesAssay, Vector

  • countOverlaps(query = GRangesAssay, subject = GRangesAssay): method for GRangesAssay, GRangesAssay

  • 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