HicAggR - In depth tutorial
Introduction | Typical workflow: | Quickstart and tutorials: | Aim: | Requirements | Installation | Load library | Test dataset | Description | 1. Genomic 3D structure | Temp directory preparation | Control condition (.hic File) | Heat shock condition (.mcool File) | 2 Genomic location and annotation data | ChIPseq peaks of Beaf-32 protein | TSS annontation | TADs annotation | Additional genome informations | Import HiC | Import | Balancing | Tips | Observed/Expected Correction | HiC data format: ContactMatrix list structure | Indexing | Example 1: Anchors from Beaf32 ChIP-seq peaks (bed file) | Example 2: Baits from TSS (transcription start sites from UCSC) | Filter indexed features: | Search Pairs | Pairing | Interactions defined with GInteraction or Pairs of GRanges. | Interactions defined with GRanges. | Case 2: Interactions around genomic regions or domains. | Regions defined with GInteraction object or Pairs of GRanges | Regions defined with GRanges | Case 3: Interactions along the chromosome axis. | Example to analyse interactions in the context of TADs: | Filtrations | Target list definition: | Example of target list: | Selection Function definition: | Example of selectionFunction according to the example target | Filtration with selection | Example of GInteraction object filtration | Example of Matrices list filtration | Specific case 1: Only one target (and therefore no selection needed) | GInteraction filtration | Matrices list filtration | Specific case 2: Sampling | GInteraction sampling | Matrices list sampling | Specific case 3: Filtration without selectionFunction | Selection function tips and examples: | Orientation | Information about the orientation | Orientation on matrices list | Orientation of one matrix only. | Prepare matrices list | Quantifications | Basic quantifications | Custom functions | Particular cases: | Values naming | One value extraction | Area extraction | Aggregations | One sample aggregation | Basic aggregation | Custom aggregation | Two samples differential aggregation | Preparation of matrices list | Aggregate | Aggregations plots | Preparation of aggregated matrices | Plots | Simple aggregation plot: | With no orientation | With Orientation | Further visualisation parameters: | Trimming aggregated values for visualisation: | Modifying color scale: | Min and max color scale | Center color scale | Change color breaks | Change color scale bias | Change color | Blurred visualization | ggplot object modifications | Session Info
Rendered fromHicAggR.Rmdusingknitr::rmarkdown