Brick_fetch_range_index {HiCBricks}R Documentation

Returns the position of the supplied ranges in the binning table associated to the Hi-C experiment.

Description

Brick_fetch_range_index constructs a ranges object using Brick_make_ranges, creates an overlap operation using GenomicRanges::findOverlaps, where the constructed ranges is the subject and the Hi-C experiment associated binning table is the query. The return of this object is a list of ranges with their corresponding indices in the binning table.

Usage

Brick_fetch_range_index(Brick, chr, start, end, names = NULL,
    type = "any")

Arguments

Brick

Required. A string specifying the path to the Brick store created with CreateBrick.

chr

Required. A character vector of length N specifying the chromosomes to select from the ranges.

start

Required. A numeric vector of length N specifying the start positions in the chromosome

end

Required. A numeric vector of length N specifying the end positions in the chromosome

names

Optional. A character vector of length N specifying the names of the chromosomes. If absent, names will take the form chr:start:end.

type

Optional. Default any Type of overlap operation to do. It should be one of two, any or within. any considers any overlap (atleast 1 bp) between the provided ranges and the binning table.

Value

Returns a GenomicRanges object of same length as the chr, start, end vectors provided. The object is returned with an additional column, Indexes. Indexes is a column of class IRanges::IntegerList, which is part of the larger IRanges::AtomicList superset. This "Indexes" column can be accessed like a normal GRanges column with the additional list accessor [[]] in place of the normal vector accessor [].

Examples


Chrom <- c("chr19","chr19")
Start <- c(1,40000)
End <- c(1000000,2000000)
Brick.file <- system.file("extdata", "test.hdf", package = "HiCBricks")
Test_Run <- Brick_fetch_range_index(Brick = Brick.file, chr = Chrom,
start = Start, end = End)
Test_Run$Indexes[[1]]


[Package HiCBricks version 1.2.0 Index]