Tests the overlap of user-supplied ranges with R-loop regions (RL regions).
rlRegionTest(object)An RLRanges object with genome "hg38".
An RLRanges object with test results accessible via
rlresult(object, "rlRegionRes").
The structure of the results is a named list containing the following:
Overlap
A tbl showing the overlap between RL regions and user-supplied ranges.
Column description:
chrom - The chromosome name
start__peaks - The starting position of the user-supplied peak in
the overlap.
end__peaks - Same as above for end position.
name__peaks - The name of the user-supplied peak in the overlap
(from names(object)).
start/end/name__rlregion - Same as above for RL regions.
strand__rlregion - The genomic strand of the RL region in the overlap.
.overlap - The size of the overlap.
Test_results
A tbl showing the results of the Fisher's exact test.
See valr::bed_fisher.
R-loop regions (RL regions) are consensus sites of R-loop formation. For
more information, see RLHub::rlregions. The rlRegionTest is a simple
function which finds the overlap of user-supplied samples with RL regions and
calculates Fisher's exact test via valr::bed_fisher.
# Example RLRanges data
rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))
# RL Region Test
rlRegionTest(rlr)
#> see ?RLHub and browseVignettes('RLHub') for documentation
#> 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
#>