Visualise methlation data from Oxford Nanopore sequencing


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Documentation for package ‘NanoMethViz’ version 2.4.2

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bsseq_to_edger Convert BSseq object to edgeR methylation matrix
bsseq_to_log_methy_ratio Convert BSseq object to log-methylation-ratio matrix
cluster_regions Cluster regions by K-means
create_tabix_file Create a tabix file using methylation calls
exons-method Nanopore Methylation Result
exons<--method Nanopore Methylation Result
exons_to_genes Convert exon annotation to genes
filter_methy Create filtered methylation file
get_example_exons_mus_musculus Get example exon annotations for mus musculus (mm10)
get_exons 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_nanomethresult Load an example NanoMethResult object
methy-method Nanopore Methylation Result
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
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
plot_gene-method Plot gene
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
plot_region-method Plot region
plot_region_heatmap Plot region methylation heatmap
plot_region_heatmap-method Plot region methylation heatmap
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 Nanopore Methylation Result
samples<--method Nanopore Methylation Result