All functions

HCT116_r1

A 4 column sparse matrix for a Hi-C matrix.

HCT116_r2

A 4 column sparse matrix for a Hi-C matrix.

HCT116_r3

A 4 column sparse matrix for a Hi-C matrix.

HCT116_r4

A 4 column sparse matrix for a Hi-C matrix.

HCT116_r5

A 4 column sparse matrix for a Hi-C matrix.

HCT116_r6

A 4 column sparse matrix for a Hi-C matrix.

Hicexp-class

An S4 class for working with Hi-C data

MD_composite()

Plot a composite MD plot with the results of a comparison

MD_hicexp()

Make MD plots for all combinations of a condition

cyclic_loess()

Cyclic Loess normalization for Hi-C data

exportJuicebox()

Export multiHiCcompare results for visualization in Juicebox

fastlo()

Perform fast loess normalization on a Hi-C experiment

hg19_cyto

A GenomicRanges object containing centromeric, gvar, and stalk regions.

hg38_cyto

A GenomicRanges object containing centromeric, gvar, and stalk regions.

hic_exactTest()

Perform exact test based difference detection on a Hi-C experiment

hic_filter()

Perform filtering on a Hi-C experiment

hic_glm()

Function to perform GLM differential analysis on Hi-C experiment

hic_scale()

Perform library scaling on a hicexp object

hic_table()

Print the hic_table

hicexp2

hicexp object with 4 samples from two groups.

hicexp_diff

hicexp object with 7 samples from two groups.

make_hicexp()

Make Hi-C experiment object from data

manhattan_hicexp()

Manhattan plot function for results of multiHiCcompare

meta()

Print the metadata

normalized()

Print the indicator for if the data is normalized

perm_test()

Perform a permutation test to check enrichment of a genomic feature with DIRs detected by multiHiCcompare

plot_counts()

Plot the count results from topDirs

plot_pvals()

Plot the p-value results from topDirs

pval_heatmap()

Function to visualize p-values from multiHiCcompare results

resolution()

Print the resolution

results()

Print the results

show(<Hicexp>)

Print information about a HiCexp object

smartApply()

Function to apply either biocParallel or standard lapply

topDirs()

Filter results of multiHiCcompare