Feature Enrichment per RL-Region (feat_enrich_rlregions) and per Sample (feat_enrich_samples).
feat_enrich_samples(quiet = FALSE) feat_enrich_rlregions(quiet = FALSE)
| quiet | If TRUE, messages are suppressed. Default: FALSE. |
|---|
A tbl object. See details.
For every R-loop-mapping sample in RLBase (feat_enrich_samples) or for
each of the three RL-Regions databases (feat_enrich_rlregions),
peaks were calculated and then
tested via RLSeq::featureEnrich() to determine enrichment within all
available genomic features.
The processing steps are described in the RLBase-data README.md.
Example data:
| db | type | num_total_peaks | num_tested_peaks | num_tested_anno_ranges | num_total_anno_ranges | avg_reldist_rl | avg_reldist_shuf | pval_reldist | stat_fisher_rl | pval_fisher_rl | stat_fisher_shuf | pval_fisher_shuf | experiment |
| Cohesin | STAG1 | 9892 | 10000 | 9935 | 9939 | 0.2514476 | 0.2480947 | 0.0816731 | 1.400271 | 0.0477869 | 0.6820876 | 0.1303705 | ERX2277510 |
| Cohesin | STAG2 | 10613 | 10000 | 9935 | 10696 | 0.2432965 | 0.2525422 | 0.0002326 | 1.945212 | 0.0000159 | 0.5382866 | 0.0174814 | ERX2277510 |
| CpG_Islands | CpG_Islands | 28189 | 10000 | 9989 | 31144 | 0.2190449 | 0.2501005 | 0.0000000 | 5.332338 | 0.0000000 | 0.9855223 | 0.9236551 | ERX2277510 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
Column description:
db - the database from which annotations were derived. See annotations.
type - the type from which annotations were derived. See annotations.
num_tested_peaks: The number of peak ranges tested for enrichment.
num_total_peaks: The total number of peaks in the sample.
num_tested_anno_ranges: The number of annotation ranges which the peaks were tested against.
num_total_anno_ranges: The total number of ranges in the annotation.
avg_reldist_rl: The mean relative distances between peaks and annotation ranges as described here.
avg_reldist_shuf: Same as avg_reldist_rl except with peaks shuffled randomly to provide a negative control.
pval_reldist: The ks.test p value from comparing the distribution of the peak and shuffle relative distances as described here.
stat_fisher_rl: The the odds ratio from the fisher's exact test as described here.
stat_fisher_shuf: Same as above, but with the shuffled peaks to provide a negative control.
pval_fisher_rl: The p value from Fisher's exact test as described here.
pval_fisher_shuf: Same as above, but with the shuffled peaks to provide a negative control.
experiment (only feat_enrich_samples()): The R-loop mapping sample for which the calculation was performed. See rlbase_samples.
opt (only feat_enrich_rlregions()): The type of RL-Region (see rlregions) which was tested.
fes <- feat_enrich_samples() fes <- feat_enrich_rlregions()