write_dmr | R Documentation |
For a quick visualization using a genome browser like IGV, this function generates [BED](https://bit.ly/1hdVNjA) and [SEG](https://bit.ly/2J2WZdZ) files of statistically significant hyper-methylated and hypo-methylated DMRs.
write_dmr(dmr_table, path, qvalue_thr = 0.05)
dmr_table |
A data.frame generated by [find_dmrs]. |
path |
A string including absolute or relative path which prefixes are added to ("_hyper.bed", "_hypo.bed", ".seg") |
qvalue_thr |
A numerical threshold. Report only DMRs with a fdr lower than threshold. |
BED files (hyper- and hypo-methylated DMRs separately) report genomic location and fdr (in form of -log10(q)). SEG files report average beta differences between tumor and normal/control samples at each DMR.
NOTE: BED files have 0-based coordinates while SEG files have 1-based coordinates.
Nothing. Only saves output tables.
## Not run: auc <- compute_AUC(tumor_example, control_example) dmr_set <- find_dmrs(tumor_example, control_example, auc, reference_example, min_sites = 10) compute_z_scores(tumor_example, control_example, dmr_set,reference_example) write_dmr(dmr_set, "dmr_set") ## End(Not run)
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