Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
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Documentation for package ‘segmenter’ version 1.15.0
Help Pages
| .Binarize | Call Java 'BinarizeBed' |
| .LearnModel | Call Java 'LearnModel' |
| accessors | Accessors for the 'segmentation' objects |
| annotate_segments | Annotate segments |
| binarize_bam | Binarize the bam files |
| binarize_bed | Binarize the bed files |
| bins | Accessors for the 'segmentation' objects |
| bins-method | Accessors for the 'segmentation' objects |
| cells | Accessors for the 'segmentation' objects |
| cells-method | Accessors for the 'segmentation' objects |
| class:segmentation | segmentation objects |
| compare_models | Compare two or more models |
| counts | Accessors for the 'segmentation' objects |
| counts-method | Accessors for the 'segmentation' objects |
| count_reads_ranges | Count reads in 'GRanges' objects from bam files |
| emission | Accessors for the 'segmentation' objects |
| emission-method | Accessors for the 'segmentation' objects |
| emissions_file | Make emissions file name |
| enrichment_files | Make enrichment file names |
| get_frequency | Get the frequency of the segments in each cell type |
| get_width | Get the width of the segments in each cell type |
| learn_model | Learn a multi-state model from chromatin data |
| likelihood | Accessors for the 'segmentation' objects |
| likelihood-method | Accessors for the 'segmentation' objects |
| markers | Accessors for the 'segmentation' objects |
| markers-method | Accessors for the 'segmentation' objects |
| merge_segments_bins | Merge segments and bins objects |
| methods | Methods to interact with 'segmentation' objects |
| model | Accessors for the 'segmentation' objects |
| model-method | Accessors for the 'segmentation' objects |
| model_file | Make model file name |
| overlap | Accessors for the 'segmentation' objects |
| overlap-method | Accessors for the 'segmentation' objects |
| overlap_files | Make overlap file names |
| plot_heatmap | Visualize the model output |
| range_bins | Format the loaded binarized data |
| range_counts | Format the loaded counts data |
| read_bam_file | Read 'bam' files |
| read_bins_file | Read 'bins' files |
| read_cellmark_file | Read 'cellmarktable' file |
| read_chromsize_file | Read 'chromsizefile' |
| read_emissions_file | Read 'emissions' file |
| read_enrichment_file | Read 'enrichment' files |
| read_model_file | Read 'modelfile' |
| read_overlap_file | Read 'segments' files |
| read_segements_file | Read 'segments' files |
| read_transitions_file | Read 'transitions' file |
| segment | Accessors for the 'segmentation' objects |
| segment-method | Accessors for the 'segmentation' objects |
| segmentation | segmentation objects |
| segmentation-class | segmentation objects |
| segments_files | Make segments file names |
| show-method | Methods to interact with 'segmentation' objects |
| states | Accessors for the 'segmentation' objects |
| states-method | Accessors for the 'segmentation' objects |
| TES | Accessors for the 'segmentation' objects |
| TES-method | Accessors for the 'segmentation' objects |
| test_obj | A segmentation object generated from the test data |
| test_objs | A a list of segmentation objects generated from the test data |
| tidy_ranges | Tidy the metadata of a 'GRanges' object |
| transition | Accessors for the 'segmentation' objects |
| transition-method | Accessors for the 'segmentation' objects |
| transitions_file | Make transitions file name |
| TSS | Accessors for the 'segmentation' objects |
| TSS-method | Accessors for the 'segmentation' objects |