featureEnrichment: Feature Enrichment

In Bishop-Laboratory/RLHub: An ExperimentHub package for accessing processed RLSuite data sets

Description

Feature Enrichment per RL-Region (feat_enrich_rlregions) and per Sample (feat_enrich_samples).

Usage

feat_enrich_samples(quiet = FALSE)

feat_enrich_rlregions(quiet = FALSE)

Arguments

quiet

If TRUE, messages are suppressed. Default: FALSE.

Details

Source

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.

Structure

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.

Value

A tbl object. See details.

Examples

fes <- feat_enrich_samples()

fes <- feat_enrich_rlregions()

Bishop-Laboratory/RLHub documentation built on Jan. 20, 2022, 3:47 p.m.