Tests the enrichment of genomic features in supplied peaks. See details.
featureEnrich(
object,
annotype = c("primary", "full"),
annotations = NULL,
downsample = 10000,
quiet = FALSE
)An RLRanges object.
The type of annotations to use. Can be one of "primary" or "full". Default: "primary". See RLHub::annotations for greater detail.
A custom annotation list of the same structure described in RLHub::annotations.
If a numeric, data will be down sampled to the requested number of peaks. This improves the speed of genomic shuffling and helps prevent p-value inflation. If FALSE, then downsampling will not be performed. Default: 10000.
If TRUE, messages will be suppressed. Default: FALSE
An RLRanges object containing the results of the enrichment test
accessed via rlresult(object, "featureEnrichment"). The results
are in tbl format. For a full description of all columns in the output
table see RLHub::feat_enrich_samples.
Annotations relevant to R-loops were curated as part of the RLBase-data workflow and are provided via RLHub::annotations.
In featureEnrich, each annotation "type" (e.g., "Exons", "Introns", etc)
is compared to the supplied RLRanges, yielding enrichment statistics with
the following procedure:
For each annotation type, the peaks are overlapped with the annotations.
Then, valr::bed_reldist is used to find the relative distance distribution between the peaks and the annotations for both the supplied RLRanges and shuffled RLRanges (via valr::bed_shuffle). Significance of the relative distance is calculated via stats::ks.test.
Then, Fisher’s exact test is implemented via valr::bed_fisher to obtain the significance of the overlap and the odds ratio.
# Example RLRanges dataset
rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))
# RL Region Test
featureEnrich(rlr)
#> see ?RLHub and browseVignettes('RLHub') for documentation
#> - Calculating enrichment...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> Warning: Not enough observations for interval tests...
#> - Done
#> GRanges object with 7 ranges and 6 metadata columns:
#> seqnames ranges strand | V4
#> <Rle> <IRanges> <Rle> | <character>
#> 1 chr14 20343155-20343313 * | /home/UTHSCSA/miller..
#> 2 chr21 8214588-8214866 * | /home/UTHSCSA/miller..
#> 3 chr21 8396653-8396835 * | /home/UTHSCSA/miller..
#> 4 chr22_KI270733v1_ran.. 129919-130080 * | /home/UTHSCSA/miller..
#> 5 chr22_KI270733v1_ran.. 174979-175184 * | /home/UTHSCSA/miller..
#> 6 chr6 52995648-52995831 * | /home/UTHSCSA/miller..
#> 7 chr9 35657778-35657976 * | /home/UTHSCSA/miller..
#> V5 V6 V7 V8 qval
#> <integer> <character> <numeric> <numeric> <numeric>
#> 1 56 . 7.40428 12.1836 5.63076
#> 2 56 . 7.27639 12.2524 5.66372
#> 3 15 . 5.19728 7.7825 1.52856
#> 4 256 . 16.31970 32.6965 25.65290
#> 5 1085 . 30.29480 116.1250 108.58400
#> 6 95 . 9.63809 16.3088 9.58453
#> 7 100 . 9.84017 16.7326 10.04910
#> -------
#> seqinfo: 640 sequences (1 circular) from hg38 genome
#>
#> RDIP-Seq +RNH1:
#> Mode: RDIP
#> Genome: hg38
#> Label: NEG
#>
#> RLSeq Results Available:
#> featureEnrichment, txFeatureOverlap, correlationMat, rlfsRes, noiseAnalysis, geneAnnoRes, predictRes, rlRegionRes
#>
#> prediction: NEG
#>
# With custom annotations
small_anno <- list(
"Centromeres" = readr::read_csv(
system.file("extdata", "Centromeres.csv.gz", package = "RLSeq"),
show_col_types = FALSE
)
)
featureEnrich(rlr, annotations = small_anno)
#> - Calculating enrichment...
#> - Done
#> GRanges object with 7 ranges and 6 metadata columns:
#> seqnames ranges strand | V4
#> <Rle> <IRanges> <Rle> | <character>
#> 1 chr14 20343155-20343313 * | /home/UTHSCSA/miller..
#> 2 chr21 8214588-8214866 * | /home/UTHSCSA/miller..
#> 3 chr21 8396653-8396835 * | /home/UTHSCSA/miller..
#> 4 chr22_KI270733v1_ran.. 129919-130080 * | /home/UTHSCSA/miller..
#> 5 chr22_KI270733v1_ran.. 174979-175184 * | /home/UTHSCSA/miller..
#> 6 chr6 52995648-52995831 * | /home/UTHSCSA/miller..
#> 7 chr9 35657778-35657976 * | /home/UTHSCSA/miller..
#> V5 V6 V7 V8 qval
#> <integer> <character> <numeric> <numeric> <numeric>
#> 1 56 . 7.40428 12.1836 5.63076
#> 2 56 . 7.27639 12.2524 5.66372
#> 3 15 . 5.19728 7.7825 1.52856
#> 4 256 . 16.31970 32.6965 25.65290
#> 5 1085 . 30.29480 116.1250 108.58400
#> 6 95 . 9.63809 16.3088 9.58453
#> 7 100 . 9.84017 16.7326 10.04910
#> -------
#> seqinfo: 640 sequences (1 circular) from hg38 genome
#>
#> RDIP-Seq +RNH1:
#> Mode: RDIP
#> Genome: hg38
#> Label: NEG
#>
#> RLSeq Results Available:
#> txFeatureOverlap, correlationMat, rlfsRes, noiseAnalysis, geneAnnoRes, predictRes, rlRegionRes
#>
#> prediction: NEG
#>