ModBamFiles             Constructor for a ModBamFiles object
ModBamFiles-class       ModBamFiles class
ModBamResult-class      Modbam methylation results
NanoMethResult-class    Nanopore Methylation Result
bsseq_to_edger          Convert BSseq object to edgeR methylation
                        matrix
bsseq_to_log_methy_ratio
                        Convert BSseq object to log-methylation-ratio
                        matrix
cluster_reads           Cluster reads based on methylation
cluster_regions         Cluster regions by K-means
create_tabix_file       Create a tabix file using methylation calls
exons_to_genes          Convert exon annotation to genes
filter_methy            Create filtered methylation file
get_cgi_mm10            Get exon annotations
get_example_exons_mus_musculus
                        Get example exon annotations for mus musculus
                        (mm10)
get_exons_homo_sapiens
                        Get exon annotations for Homo sapiens (hg19)
get_exons_mus_musculus
                        Get exon annotations for Mus musculus (mm10)
load_example_modbamresult
                        Load an example ModBamResult object
load_example_nanomethresult
                        Load an example NanoMethResult object
methy_col_names         Column names for methylation data
methy_to_bsseq          Create BSSeq object from methylation tabix file
methy_to_edger          Convert NanoMethResult object to edgeR
                        methylation matrix
modbam_to_tabix         Convert BAM with modifications to tabix format
plot_agg_genes          Plot gene aggregate plot
plot_agg_regions        Plot aggregate regions
plot_gene               Plot gene methylation
plot_gene_heatmap       Plot gene methylation heatmap
plot_grange             Plot GRanges
plot_grange_heatmap     Plot GRanges heatmap
plot_mds                Plot MDS
plot_pca                Plot PCA
plot_region             Plot region methylation
plot_region_heatmap     Plot region methylation heatmap
plot_violin             Plot violin for regions
query_exons             Query exons
query_methy             Query methylation data
region_methy_stats      Calculate region methylation statistics
