Perform Chromatin Segmentation Analysis in R by Calling ChromHMM


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Documentation for package ‘segmenter’ version 1.0.0

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.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