# Visualise methylation data from Oxford Nanopore sequencing

## Documentation for package ‘NanoMethViz’ version 3.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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-method | Modbam methylation results
exons-method | Nanopore Methylation Result
exons<--method | Modbam methylation results
exons<--method | Nanopore Methylation Result
exons_to_genes | Convert exon annotation to genes
filter_methy | Create filtered methylation file
get_cgi_grcm39 | Get exon annotations
get_cgi_hg19 | Get exon annotations
get_cgi_hg38 | Get exon annotations
get_cgi_mm10 | Get exon annotations
get_example_exons_mus_musculus | Get example exon annotations for mus musculus (mm10)
get_exons | Get exon annotations
get_exons_grcm39 | Get exon annotations
get_exons_hg19 | Get exon annotations
get_exons_hg38 | Get exon annotations
get_exons_homo_sapiens | Get exon annotations for Homo sapiens (hg19)
get_exons_mm10 | Get exon annotations
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-method | Modbam methylation results
methy-method | Nanopore Methylation Result
methy<--method | Modbam methylation results
methy<--method | Nanopore Methylation Result
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
ModBamFiles | Constructor for a ModBamFiles object
ModBamFiles-class | ModBamFiles class
ModBamResult | Modbam methylation results
ModBamResult-class | Modbam methylation results
modbam_to_tabix | Convert BAM with modifications to tabix format
mod_code-method | Modbam methylation results
mod_code<--method | Modbam methylation results
NanoMethResult | Nanopore Methylation Result
NanoMethResult-class | Nanopore Methylation Result
plot_agg_genes | Plot gene aggregate plot
plot_agg_regions | Plot aggregate regions
plot_gene | Plot gene methylation
plot_gene-method | Plot gene methylation
plot_gene_heatmap | Plot gene methylation heatmap
plot_gene_heatmap-method | 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-method | Plot region methylation
plot_region_heatmap | Plot region methylation heatmap
plot_region_heatmap-method | Plot region methylation heatmap
plot_violin | Plot violin for regions
query_exons | Query exons
query_exons_gene_id | Query exons
query_exons_region | Query exons
query_exons_symbol | Query exons
query_methy | Query methylation data
region_methy_stats | Calculate region methylation statistics
samples-method | Modbam methylation results
samples-method | Nanopore Methylation Result
samples<--method | Modbam methylation results
samples<--method | Nanopore Methylation Result
show-method | Constructor for a ModBamFiles object