Brick_fetch_range_index {HiCBricks} | R Documentation |
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.
Brick_fetch_range_index(Brick, chr, start, end, names = NULL, type = "any")
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. |
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 [].
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]]