Extract Overlap Groups from Genomic or Set Overlap Results
Source:R/extractOverlaps.R
extractOverlaps.RdThis function extracts subsets of intersecting elements grouped by their
overlap category (e.g., "110").
For genomic overlaps, it returns a GRangesList; for set overlaps, it
returns a named list of character vectors.
Value
A named list of grouped intersecting elements:
If input is a
GenomicOverlapsResult, aGRangesListsplit byintersect_category.If input is a
SetOverlapsResult, a namedlistof character vectors grouped byintersect_category.
Examples
# Example with gene sets (built-in dataset)
data(gene_list)
res_sets <- computeOverlaps(gene_list)
group_gene <- extractOverlaps(res_sets)
group_gene
#> $group_001
#> [1] "ACTN1" "ALDOA" "CRYBG1" "AK4" "ACYP2" "AFP" "ACTN2" "AMPD3"
#> [9] "ACADS" "ACY1" "ADH1B" "ACTBP7" "ADH6" "ACTBP4" "ANXA2" "AGXT"
#> [17] "TLE5"
#>
#> $group_010
#> [1] "AFM" "ADPRH" "AIF1" "ACVR2A" "ACTA1" "PLIN2"
#> [7] "ALDH1A3" "ALK" "ACTG2" "ADCY8" "ABR" "ADCYAP1"
#> [13] "ADRA2A" "ADORA2B" "ADRA1B" "ANXA5" "ACLY" "ANK3"
#> [19] "ADCY6" "ACR" "ADAM10" "AARS1" "ACVR2B" "ACO2"
#> [25] "ADH1C" "PARP1" "ADD2" "ADARB1" "ADCY2" "ANXA1"
#> [31] "ALCAM" "ADORA2A" "AMFR" "AMBN" "NAT2" "A1BG"
#> [37] "ACADL" "ADH5" "ACTG1P8" "AADAC" "ACOX1" "ALDH9A1"
#> [43] "ANXA2P2" "ADORA2BP1" "ADRB3"
#>
#> $group_100
#> [1] "ALPP" "ACTG1P9" "AHSG" "ASIC2" "ACTG1P10" "ALAS1"
#> [7] "AKT2" "PARP1P1" "ABCD1" "SLC25A6" "AAMP" "ADCP1"
#> [13] "ACADVL" "ACTG1" "ANGPT2" "AGTR1" "ACACB" "ACTBP9"
#> [19] "ALDH1B1" "ADAR" "ABCD2" "AMHR2" "ABCB7" "ABCA1"
#> [25] "PARP4" "ACTG1P1" "JAG1" "ACTA2" "ADH7" "AP1B1"
#> [31] "ACVR1" "ACTN4" "A2MP1" "ABCA4" "ALAD" "ADRA1A"
#> [37] "ADCY5" "ALDOB" "AP2B1" "AMELY" "ABL1" "ACTC1"
#> [43] "AK2" "ALOX12B" "ACTN3" "AIC" "ALB" "NATP"
#> [49] "ANG" "AHR" "ABCA2" "ALPL" "ANXA2P1" "AMELX"
#> [55] "AHCY" "PARP1P2" "ALOX5" "AMPD1" "AFA" "ACADSB"
#> [61] "AIH3" "ACAN" "AGA" "AMY1C" "ADSS2" "ALDH2"
#> [67] "ALOX15B"
#>
#> $group_011
#> [1] "AMY1A" "ACRV1" "ALAS2" "ABCA3" "ALPG" "AMY2A" "ADH4" "ADARB2"
#> [9] "NR0B1" "AMYP1" "A2M" "AGTR2" "ALOX15" "ACP1" "ADH1A" "AF8T"
#>
#> $group_101
#> [1] "NAT1" "ACAA1" "AGT" "AMD1P2"
#>
#> $group_110
#> [1] "ADRB1" "ABAT" "ALOX5AP" "ADD1" "ACVR1B" "AANAT"
#> [7] "ADSL" "ADCY7" "ALX3" "ALOX12P1" "ANGPT1" "ACTG1P6"
#> [13] "ADAM8" "ACHE" "ANCR" "ACP3" "ACP5" "APLNR"
#> [19] "ACTBP8" "ADCY1" "ADA"
#>
#> $group_111
#> [1] "ACP2" "ALDH3A1" "ACTB" "ACACA" "ASIC1" "SLC25A5"
#> [7] "ACTL6A" "AMY2B" "AMH" "AMPH" "ADK" "ALDH3A2"
#> [13] "ACTG1P3" "ACO1" "ACTG1P7" "ALPI" "ANXA4" "AGL"
#> [19] "ADRB2" "ABCF1" "ABO" "AMD1" "ALS3" "ALOX12"
#> [25] "AMBP" "AMPD2" "ALDH1A1" "AFG3L1P" "ADFN" "ADCYAP1R1"
#> [31] "ADD3" "ALOX12P2" "BIN1"
#>
# Example with genomic regions (built-in dataset)
data(a549_chipseq_peaks)
res_genomic <- computeOverlaps(a549_chipseq_peaks)
group_genomic <- extractOverlaps(res_genomic)
group_genomic
#> GRangesList object of length 7:
#> $group_010
#> GRanges object with 267 ranges and 1 metadata column:
#> seqnames ranges strand | intersect_category
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr7 234690-235402 * | 010
#> [2] chr7 538240-538633 * | 010
#> [3] chr7 1504294-1504733 * | 010
#> [4] chr7 1506830-1507301 * | 010
#> [5] chr7 1513353-1513690 * | 010
#> ... ... ... ... . ...
#> [263] chr7 155618941-155619523 * | 010
#> [264] chr7 155644241-155644737 * | 010
#> [265] chr7 158829343-158830028 * | 010
#> [266] chr7 158856251-158856723 * | 010
#> [267] chr7 159012435-159013222 * | 010
#> -------
#> seqinfo: 24 sequences from an unspecified genome; no seqlengths
#>
#> ...
#> <6 more elements>