A collection of genome masks for use with analyzeRLFS. See the
data-raw/genome_masks.R script for the processing steps.
genomeMasksAn object of class list of length 8.
genomeMasks is a named list of GRanges objects. Each entry in the
list follows the naming convention: <genome>.masked, where <genome>
is an official UCSC genome ID. Each entry contains
a GRanges object with the masked ranges from <genome>. The genomes
provided correspond to the masked genomes available in
BSgenome::available.genomes.
genomeMasks
#> $apiMel2.masked
#> GRanges object with 16164 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] Group1 8604-9586 *
#> [2] Group1 45114-45303 *
#> [3] Group1 74031-74436 *
#> [4] Group1 127756-127879 *
#> [5] Group1 129251-129560 *
#> ... ... ... ...
#> [16160] GroupUn 320949657-320984656 *
#> [16161] GroupUn 320985744-321020743 *
#> [16162] GroupUn 321029717-321064716 *
#> [16163] GroupUn 321065873-321100872 *
#> [16164] GroupUn 321103175-321138174 *
#> -------
#> seqinfo: 17 sequences from apiMel2 genome
#>
#> $canFam3.masked
#> GRanges object with 19553 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1-100 *
#> [2] chr1 24126-27778 *
#> [3] chr1 45598-45882 *
#> [4] chr1 89487-89496 *
#> [5] chr1 91795-162650 *
#> ... ... ... ...
#> [19549] chrX 123311357-123312638 *
#> [19550] chrX 123445883-123445892 *
#> [19551] chrX 123776002-123776553 *
#> [19552] chrX 123821636-123822296 *
#> [19553] chrX 123845565-123845574 *
#> -------
#> seqinfo: 40 sequences (1 circular) from canFam3 genome
#>
#> $danRer7.masked
#> GRanges object with 24170 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 508054-508153 *
#> [2] chr1 509073-509172 *
#> [3] chr1 509982-510081 *
#> [4] chr1 512882-512981 *
#> [5] chr1 513539-513638 *
#> ... ... ... ...
#> [24166] chr25 38489453-38489552 *
#> [24167] chr25 38492045-38492144 *
#> [24168] chr25 38493834-38493933 *
#> [24169] chr25 38495078-38495177 *
#> [24170] chr25 38498098-38498197 *
#> -------
#> seqinfo: 26 sequences (1 circular) from danRer7 genome
#>
#> $galGal4.masked
#> GRanges object with 9258 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1034-1133 *
#> [2] chr1 1635-1734 *
#> [3] chr1 2505-2604 *
#> [4] chr1 3124-3223 *
#> [5] chr1 4729-4828 *
#> ... ... ... ...
#> [9254] chrLGE22C19W28_E50C23 923755-937231 *
#> [9255] chrLGE22C19W28_E50C23 939390-939489 *
#> [9256] chrLGE22C19W28_E50C23 940663-940900 *
#> [9257] chrLGE22C19W28_E50C23 942958-943949 *
#> [9258] chrLGE22C19W28_E50C23 961456-962294 *
#> -------
#> seqinfo: 34 sequences (1 circular) from galGal4 genome
#>
#> $hg19.masked
#> GRanges object with 460 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1-10000 *
#> [2] chr1 177418-227417 *
#> [3] chr1 267720-317719 *
#> [4] chr1 471369-521368 *
#> [5] chr1 2634221-2684220 *
#> ... ... ... ...
#> [456] chr19_gl949751_alt 789619-815618 *
#> [457] chr19_gl949752_alt 253363-258362 *
#> [458] chr19_gl949753_alt 195632-213631 *
#> [459] chr19_gl949753_alt 361078-363077 *
#> [460] chr19_gl949753_alt 509415-609414 *
#> -------
#> seqinfo: 298 sequences (2 circular) from hg19 genome
#>
#> $hg38.masked
#> GRanges object with 1024 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1-10000 *
#> [2] chr1 207667-257666 *
#> [3] chr1 297969-347968 *
#> [4] chr1 535989-585988 *
#> [5] chr1 2702782-2746290 *
#> ... ... ... ...
#> [1020] chr19_KV575258v1_alt 106475-106477 *
#> [1021] chr19_KV575258v1_alt 106479-106481 *
#> [1022] chr19_KV575258v1_alt 106484-106485 *
#> [1023] chr19_KV575260v1_alt 62709-62710 *
#> [1024] chr19_KV575260v1_alt 70481-70482 *
#> -------
#> seqinfo: 595 sequences (1 circular) from hg38 genome
#>
#> $mm10.masked
#> GRanges object with 587 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1-3000000 *
#> [2] chr1 3002130-3003118 *
#> [3] chr1 22424868-22424967 *
#> [4] chr1 22433269-22466510 *
#> [5] chr1 75055557-75121556 *
#> ... ... ... ...
#> [583] chrUn_GL456393 53788-53887 *
#> [584] chrUn_GL456394 1035-2612 *
#> [585] chrUn_GL456394 20897-21977 *
#> [586] chrUn_GL456396 7730-8220 *
#> [587] chrUn_GL456396 11697-11940 *
#> -------
#> seqinfo: 66 sequences (1 circular) from mm10 genome
#>
#> $mm9.masked
#> GRanges object with 1025 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1-3000000 *
#> [2] chr1 22414949-22415048 *
#> [3] chr1 22423350-22473349 *
#> [4] chr1 24686639-24736638 *
#> [5] chr1 75102131-75118130 *
#> ... ... ... ...
#> [1021] chrUn_random 5884087-5884186 *
#> [1022] chrUn_random 5892169-5892268 *
#> [1023] chrUn_random 5894720-5896266 *
#> [1024] chrUn_random 5897640-5897925 *
#> [1025] chrUn_random 5898884-5899265 *
#> -------
#> seqinfo: 35 sequences (1 circular) from mm9 genome
#>