Package index • HicAggR

Data

Test datasets.

Beaf32_Peaks.gnr: D.melanogaster Beaf-32 ChIP-seq.

TSS_Peaks.gnr: D.melanogaster Transcription starting sites.

TADs_Domains.gnr: D.melanogaster TADs.

HiC_Ctrl.cmx_lst: In situ Hi-C control.

HiC_HS.cmx_lst: In situ Hi-C heat treated.

HiC

Functions for HiC data preprocessing.

GetInfo(): get some basic information about your hic file

BalanceHiC(): Compute HiC matrix-balancing.

CutHiC(): Cut HiC map in chunks.

ImportHiC(): Import Hic data

ICEnorm(): Compute Iterative Correction.

JoinHiC(): Merge HiC chunk.

OverExpectedHiC(): Genomic distance bias correction.

SwitchMatrix(): Change values of HiC map.

VCnorm(): Compute Vanilla Count Correction.

GenomicRanges adding

Additional functions for GRanges objects.

BinGRanges(): Bin a GRanges.

GenomicSystem(): Base pairs convertion.

IndexFeatures(): Indexes GRanges on genome.

MergeGRanges(): Merge GRanges.

SeqEnds(): Get all sequences lengths.

StrToGRanges(): Convert String to GRanges.

Aggregation Analysis

Functions for performing an aggregation analysis.

PrepareMtxList(): Prepare matrices list for further analysis.

Aggregation(): Aggregation of matrices list.

ExtractSubmatrix(): Submatrix extraction.

FilterInteractions(): Submatrix or Interactions filtering.

GetQuantif(): Compute quantification on extracted submatrices.

OrientateMatrix(): Matrix orientation

SearchPairs(): Creates pairs from genomic index.

Visualisation

Functions for visualising aggregation analysis results.

ggAPA(): Aggregation plot

Hue(): Hue palette.

viridis(): viridis palette.

YlGnBu(): YlGnBu palette.

YlOrRd(): YlOrRd palette.

PlotAPA(): Draw aggregation plot.

plotMultiAPA(): Draw aggregation plots for interactions with different distances.

preparePlotgardener(): preparePlotgardener

Additional Helpful Functions

Function to import loops in bedpe format and to compare your couples values with background less plausible couples

ImportLoops(): ImportLoops: import called loops in .bedpe format to use in HicAggR

CompareToBackground(): CompareToBackground