LoopRig (version 0.1.1)

ScaffoldElements: Finds elements within loops scaffolded by another set of elements

Description

Using a finalized LoopRanges loops object and two sets of elements, determines which loops are 'anchored' by the first set of elements (x) and finds which elements from the second set (y) are within these loops.

Usage

ScaffoldElements(loop_ranges, element_ranges_x, element_ranges_y,
  range_out_x = FALSE, range_out_y = FALSE, overlap_threshold = 1)

Arguments

loop_ranges

A single LoopRanges object that has been subset to one range through ConsensusLoops().

element_ranges_x

The first element ranges to be considered. If using an 'ElementRanges' class object, subset by using list indexing.

element_ranges_y

The second element ranges to be considered. If using an 'ElementRanges' class object, subset by using list indexing.

range_out_x

A boolean indicating if the output should be a subset element ranges object for element_ranges_x instead of the default dataframe. (default = FALSE)

range_out_y

A boolean indicating if the output should be a subset element ranges object for element_ranges_y instead of the default dataframe. (default = FALSE)

overlap_threshold

Single numerical input for significant base-pair overlap to be considered 'overlapping'. Default is 1 base-pair.

Value

Returns a dataframe indicating scaffold linked elements in the form of their first metadata columns and the loop IDs for their scaffolds. The element_ranges_x (scaffold) are always under column 1, and element_ranges_y (links) are always under column 2.

Examples

# NOT RUN {
# Load enhancer and promoter elements into an ElementRanges object
enhancers <- system.file("extdata/elements", "enhancers.bed", package = "LoopRig", mustWork = TRUE)
promoters <- system.file("extdata/elements", "promoters.bed", package = "LoopRig", mustWork = TRUE)
element_ranges <- ElementsToRanges(enhancers, promoters, 
element_names = c("enhancers", "promoters"), 
custom_cols = 1, custom_mcols = 4)

# Load loops into LoopRanges object and determine consensus loops
ovary_loops <- system.file("extdata/loops", "ovary_hg19.bedpe", 
package = "LoopRig", mustWork = TRUE)
pancreas_loops <- system.file("extdata/loops", "pancreas_hg19.bedpe", 
package = "LoopRig", mustWork = TRUE)
loops <- LoopsToRanges(ovary_loops, pancreas_loops, custom_cols = 0)
consensus_loops <- ConsensusLoops(loops)

# Based on consensus loops, determine which loops are anchored by enhancers and which 
# promoters are overlapping with these loops
ScaffoldElements(consensus_loops, element_ranges[[1]], element_ranges[[2]])   
# }