View source: R/Brick_functions.R
Brick_get_ranges | R Documentation |
Brick_get_ranges
will get a ranges object if present in the Brick store
and return a GRanges object.
Brick_get_ranges(Brick = NA, chr = NA, rangekey = NA, resolution = NA)
Brick |
Required. A string specifying the path to the Brick store created with Create_many_Brick. |
chr |
Optional. A chr string specifying the chromosome to select from the ranges. |
rangekey |
Required. A string specifying the name of the ranges. |
resolution |
Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed |
If a rangekey is present, the ranges will be retrieve and a GRanges constructed. Metadata columns will also be added. If these are rangekeys other than "Bintable", and had been added using Brick_add_ranges the width and Strand columns may appear as metadata columns. These will most likely be artifacts from converting the original ranges object to a data.frame.
Returns a GRanges object with the associated metadata columns that may have been present in the Ranges object.
Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"), package = "HiCBricks") out_dir <- file.path(tempdir(), "list_get_ranges_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) Brick_get_ranges(Brick = My_BrickContainer, chr = "chr2L", rangekey = "Bintable", resolution = 100000)
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