determine_anchor_overlap: Identifies Overlapping Anchors

In kkrismer/idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Identifies Overlapping Anchors

Description

Identifies all overlapping anchor pairs (m:n mapping).

Usage

determine_anchor_overlap(rep1_anchor, rep2_anchor, max_gap = -1L)

Arguments

rep1_anchor	data frame with the following columns: column 1: chr character; genomic location of anchor in replicate 1 - chromosome (e.g., "chr3") column 2: start integer; genomic location of anchor in replicate 1 - start coordinate column 3: end integer; genomic location of anchor in replicate 1 - end coordinate
rep2_anchor	data frame with the following columns: column 1: chr character; genomic location of anchor in replicate 2 - chromosome (e.g., "chr3") column 2: start integer; genomic location of anchor in replicate 2 - start coordinate column 3: end integer; genomic location of anchor in replicate 2 - end coordinate
max_gap	integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

A data frame containing overlapping anchor pairs with the following columns:

column 1:	rep1_idx	anchor index in data frame rep1_anchor
column 2:	rep2_idx	anchor index in data frame rep2_anchor

Examples

rep1_df <- idr2d:::chiapet$rep1_df
rep2_df <- idr2d:::chiapet$rep2_df

rep1_anchor_a <- data.frame(chr = rep1_df[, 1],
                            start = rep1_df[, 2],
                            end = rep1_df[, 3])
rep2_anchor_a <- data.frame(chr = rep2_df[, 1],
                            start = rep2_df[, 2],
                            end = rep2_df[, 3])

anchor_a_overlap <- determine_anchor_overlap(rep1_anchor_a, rep2_anchor_a)

kkrismer/idr2d documentation built on Feb. 7, 2024, 2:23 p.m.