cluster_reads function

[wietingj]

Hello,

I would like to cluster reads based on mod_prob results, as the plot_region() result of my mbr data showed some drifting apart of "spaghettis" in a particular region, independent of experimental group assignment.

I thought the cluster_reads() function listed in the NanoMethViz reference manual might be a useful tool for this. However, this function does not seem to be included in the current version. Could you have a look?

Or is there a better way to filter reads based on mod_prob in a specific region and replot those reads colour-coded by cluster assignment?

Thanks for your help!

Describe the bug

packageVersion("NanoMethViz") [1] ‘3.0.2’ cluster_reads(x, chr, start, end, min_pts = 5) Error in cluster_reads(x, chr, start, end, min_pts = 5) : could not find function "cluster_reads" ls("package:NanoMethViz") [1] "bsseq_to_edger" "bsseq_to_log_methy_ratio"
[3] "cluster_regions" "create_tabix_file"
[5] "exons" "exons_to_genes"
[7] "exons<-" "filter_methy"
[9] "get_example_exons_mus_musculus" "get_exons_grcm39"
[11] "get_exons_hg19" "get_exons_hg38"
[13] "get_exons_homo_sapiens" "get_exons_mm10"
[15] "get_exons_mus_musculus" "load_example_modbamresult"
[17] "load_example_nanomethresult" "methy"
[19] "methy_col_names" "methy_to_bsseq"
[21] "methy_to_edger" "methy<-"
[23] "mod_code" "mod_code<-"
[25] "modbam_to_tabix" "ModBamFiles"
[27] "ModBamResult" "NanoMethResult"
[29] "plot_agg_genes" "plot_agg_regions"
[31] "plot_gene" "plot_gene_heatmap"
[33] "plot_grange" "plot_grange_heatmap"
[35] "plot_mds" "plot_pca"
[37] "plot_region" "plot_region_heatmap"
[39] "plot_violin" "query_exons_gene_id"
[41] "query_exons_region" "query_exons_symbol"
[43] "query_methy" "region_methy_stats"
[45] "samples" "samples<-"
[47] "show" "sigmoid"

Session info

sessionInfo() R version 4.4.0 (2024-04-24) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] NanoMethViz_3.0.2 ggplot2_3.5.1