Irreproducible Discovery Rate for Genomic Interactions Data

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Documentation for package ‘idr2d’ version 1.19.0

• 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