# Irreproducible Discovery Rate for Genomic Interactions Data

## Documentation for package ‘idr2d’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calculate_midpoint_distance1d | Distance between Midpoints of two Peaks
calculate_midpoint_distance2d | Distance between Anchor Midpoints of two Interactions
calculate_relative_overlap1d | Relative Anchor Overlap of two Peaks
calculate_relative_overlap2d | Relative Anchor Overlap of two Interactions
chiapet | Example Genomic Interaction Data Set
chipseq | Example Genomic Peak Data Set
determine_anchor_overlap | Identifies Overlapping Anchors
draw_hic_contact_map | Create Hi-C contact map
draw_idr_distribution_histogram | Create histogram of IDR values
draw_rank_idr_scatterplot | Create scatterplot of IDR values
draw_value_idr_scatterplot | Create scatterplot of IDR values
establish_bijection | Finds One-to-One Correspondence between Peaks or interactions from Replicate 1 and 2
establish_bijection1d | Finds One-to-One Correspondence between Peaks from Replicate 1 and 2
establish_bijection2d | Finds One-to-One Correspondence between Interactions from Replicate 1 and 2
establish_overlap1d | Establish m:n Mapping Between Peaks from Replicate 1 and 2
establish_overlap2d | Establish m:n mapping between interactions from replicate 1 and 2
estimate_idr | Estimates IDR for Genomic Peaks or Genomic Interactions
estimate_idr1d | Estimates IDR for Genomic Peak Data
estimate_idr2d | Estimates IDR for Genomic Interaction Data
estimate_idr2d_hic | Estimates IDR for Genomic Interactions measured by Hi-C experiments
hic | Example Hi-C data set
parse_hic_pro_matrix | Parse .matrix and .bed files from HiC-Pro for IDR2D analysis
parse_juicer_matrix | Parse .hic files from Juicer for IDR2D analysis
preprocess | Prepares Data for IDR Analysis
remove_nonstandard_chromosomes1d | Removes Peaks on Non-standard Chromosomes
remove_nonstandard_chromosomes2d | Removes Interactions on Non-standard Chromosomes