Package index • NanoMethViz

Package

NanoMethViz NanoMethViz-package: NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

Plotting Regions

plot_gene(): Plot gene methylation

plot_gene_heatmap(): Plot gene methylation heatmap

plot_region(): Plot region methylation

plot_region_heatmap(): Plot region methylation heatmap

plot_grange(): Plot GRanges

plot_grange_heatmap(): Plot GRanges heatmap

Other Plots

plot_agg_genes(): Plot gene aggregate plot

plot_agg_regions(): Plot aggregate regions

plot_mds(): Plot MDS

plot_pca(): Plot PCA

plot_violin(): Plot violin for regions

Feature Annotations

get_cgi_mm10() get_cgi_grcm39() get_cgi_t2t() get_cgi_hg19() get_cgi_hg38() get_exons_mm10() get_exons_grcm39() get_exons_hg19() get_exons_hg38() get_exons_t2t(): Get exon annotations

get_exons_homo_sapiens(): Get exon annotations for Homo sapiens (hg19)

get_exons_mus_musculus(): Get exon annotations for Mus musculus (mm10)

exons_to_genes(): Convert exon annotation to genes

Conversion

bsseq_to_edger(): Convert BSseq object to edgeR methylation matrix

bsseq_to_log_methy_ratio(): Convert BSseq object to log-methylation-ratio matrix

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

Querying Methylation Data

query_methy(): Query methylation data

filter_methy(): Create filtered methylation file

Data Objects

NanoMethResult() methy(<NanoMethResult>) `methy<-`(<NanoMethResult>,<ANY>) samples(<NanoMethResult>) `samples<-`(<NanoMethResult>,<data.frame>) exons(<NanoMethResult>) `exons<-`(<NanoMethResult>,<data.frame>): Nanopore Methylation Result

methy(<ModBamResult>) `methy<-`(<ModBamResult>,<ModBamFiles>) samples(<ModBamResult>) `samples<-`(<ModBamResult>,<data.frame>) exons(<ModBamResult>) `exons<-`(<ModBamResult>,<data.frame>) mod_code(<ModBamResult>) `mod_code<-`(<ModBamResult>,<character>) ModBamResult(): Modbam methylation results

ModBamFiles() show(<ModBamFiles>): Constructor for a ModBamFiles object

ModBamFiles-class: ModBamFiles class

methy(): Get methylation data

samples(): Get sample annotation

exons(): Get exon annotation

query_exons_region() query_exons_gene_id() query_exons_symbol(): Query exons

create_tabix_file(): Create a tabix file using methylation calls

Example Data

load_example_modbamresult(): Load an example ModBamResult object

load_example_nanomethresult(): Load an example NanoMethResult object

get_example_exons_mus_musculus(): Get example exon annotations for mus musculus (mm10)

Miscallaneous

region_methy_stats(): Calculate region methylation statistics

cluster_regions(): Cluster regions by K-means

cluster_reads(): Cluster reads based on methylation

methy_col_names(): Column names for methylation data