Visualise methylation data from Oxford Nanopore sequencing

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Documentation for package ‘NanoMethViz’ version 3.2.0

• 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