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 = NA,
        chr = NA,
        start = NA,
        end = NA,
        names = NA,
        resolution = NA,
        type = "any"
    )

### Arguments

`Brick` | Required. A string specifying the path to the Brick store created with Create_many_Brick.
`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.
`resolution` | Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
`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

    Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"),
    package = "HiCBricks")

    out_dir <- file.path(tempdir(), "fetch_range_index_test")
    dir.create(out_dir)

    My_BrickContainer <- Create_many_Bricks(BinTable = Bintable.path,
      bin_delim = " ", output_directory = out_dir, file_prefix = "Test",
      experiment_name = "Vignette Test", resolution = 100000,
      remove_existing = TRUE)

    Chrom <- c("chr2L","chr2L")
    Start <- c(1,40000)
    End <- c(1000000,2000000)

    Test_Run <- Brick_fetch_range_index(Brick = My_BrickContainer,
    chr = Chrom, start = Start, end = End, resolution = 100000)
    Test_Run$Indexes[[1]]

[Package HiCBricks version 1.10.0 Index]