bestOverlap-methods: Find the best overlap between GRanges

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Find the best overlap between GRanges

Description

Find the best overlap between ranges

Usage

bestOverlap(x, y, ...)

## S4 method for signature 'GRanges,GRanges'
bestOverlap(
  x,
  y,
  var = NULL,
  ignore.strand = FALSE,
  missing = NA_character_,
  min_prop = 0.01,
  ...
)

## S4 method for signature 'GRanges,GRangesList'
bestOverlap(
  x,
  y,
  ignore.strand = FALSE,
  missing = NA_character_,
  min_prop = 0.01,
  ...
)

Arguments

x	a GRanges object
y	a named GRangesList or GRanges object with mcol as reference category
...	Not used
var	The variable to use as the category. Not required if y is a GRangesList
ignore.strand	logical(1) Passed to findOverlaps
missing	Value to assign to ranges with no overlap
min_prop	Threshold below which overlaps are discarded

Details

This finds the category in the subject GRanges (y) which has the best overlap with the query GRanges (x). The aim is to produce a character vector for best classifying the query GRanges using an external set of features (e.g. promoters, enhancers etc). If the subject (y) is a GRanges object, the values in the specified column will be used as the category. If the subject (y) is a GRangesList, the names of the list will be used to provide the best match

Value

Character vector the same length as the supplied GRanges object

Examples

gr <- GRanges("chr1:1-10")
gr_cat <- GRanges(c("chr1:2-10", "chr1:5-10"))
gr_cat$category <- c("a", "b")
propOverlap(gr, gr_cat)
bestOverlap(gr, gr_cat, var = "category")

grl <- splitAsList(gr_cat, gr_cat$category)
lapply(grl, function(x) propOverlap(gr, x))
bestOverlap(gr, grl)

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.