Man pages for LTLA/fugi
Further Utilities for Genomic Interactions
| annotateInteractions | Annotate interactions |
| annotateRegions | Annotate regions |
| asBED | Coerce to BED structure |
| availableDisplayPars | Available display parameters |
| calculateDistances | Calculate interaction distances |
| capitalize | Capitalize first letter of string |
| categoriseInteractions | Categorize interaction types |
| countsBetweenAnchors-methods | Summarise interactions between anchors |
| dot-importHicLib | Function to read in processed Hi-C interaction data generated... |
| dot-importHomer | Function to read in processed Hi-C interaction data generated... |
| dot-processChiapetName | Function to process names relating to interactions stored in... |
| dot-readBam | Function to read in interaction-data stored in a BAM file |
| dot-readTwoBams | Function to read in interaction-data stored in a pair of BAM... |
| dot-validateInput | Function to validate tabular input |
| export.bed12 | Export interactions in BED12 format |
| export.bedpe | Export interactions in BEDPE format. |
| export.chiasig | Export interactions in a BEDPE-like format for use with... |
| export.igraph | Export interactions to an igraph object |
| fugi-package | fugi: Further utitilies for Genomic Interactions |
| get_binom_ligation_threshold | Get self ligation threshold |
| get_self_ligation_threshold | Get self ligation threshold |
| getters | Functions to access data in a GenomicInteractions object |
| hg19.refseq.transcripts | Human Refseq transcripts from chr 17-18 |
| hic_example_data | Example HiC dataset |
| InteractionHelpers | Interaction type helper functions |
| InteractionTrack | Constructor to create an InteractionTrack object |
| InteractionTrack-class | The InteractionTrack class |
| makeGenomicInteractionsFromFile | Create GenomicInteraction objects from a file |
| mm9_refseq_promoters | Mouse Refseq promoters from chr 14-15 |
| plotAvgViewpoint | Plot coverage around a set of virtual 4C viewpoints |
| plotCisTrans | Plot cis/trans percentages |
| plotCounts | Plot interaction count frequency |
| plotDists | Cis interaction distances |
| plotInteractionAnnotations | Plot interaction types |
| plotSummaryStats | Plot summary statistics |
| plotViewpoint | Plot coverage around a virtual 4C viewpoint |
| removeDups | Remove duplicated interactions |
| resetAnnotations | Reset annotations |
| sameStrand | Check if anchors have the same strand |
| setters | Functions to set interaction data |
| subsetByFeatures | Subset a GenomicInteractions object by features |
| sum-GenomicInteractions-method | Return the total number of interactions in a... |
| summariseByFeaturePairs | Summarise by feature pairs |
| summariseByFeatures | Summarize by features |
| thymus_enh | Putative enhancers from mouse thymus data |
| viewPoint | Virtual 4C viewpoint |
