tre <- GenomicRanges::GRanges(
c(
"chr1:5001-5500:*", # Enhancer
"chr1:9900-10100:*", # Partially overlaps gene 1
"chr1:10101-10300:*", # Overlaps gene 1
"chr1:25001-25500:*", # Enhancer
"chr1:39901-40100:*", # Partially overlaps gene 2
"chr1:39701-39900:*" # Overlaps gene 2
),
tre_id = 1:6
)
genes_overlapping <- GenomicRanges::GRanges(
c(
"chr1:10001-15000:+",
"chr1:15000-20000:+", # Overlaps with gene above.
"chr1:30001-40000:-"
),
gene_id = 1:3)
genes <- GenomicRanges::GRanges(
c(
"chr1:10001-15000:+",
"chr1:30001-40000:-"
),
gene_id = 1:2)
tss <- GenomicRanges::GRanges(
c(
## TSSs related to gene 1 chr:10000-15000+ (# nolint)
"chr1:9801-9900:-", # uaRNA.
"chr1:9902-10001:-", # uaRNA overlaps with promoter.
"chr1:9900-10100:-", # aRNA overlaps with promoter.
"chr1:10001-10200:-", # daTSS that overlaps with promoter.
"chr1:10101-10300:+", # Alternative TSS at 100 bp.
"chr1:10101-10300:-", # daTSS at 100 bp.
"chr1:10301-10400:-", # daTSS at 300 bp.
"chr1:10501-10600:-", # daRNA at 500 bp.
## TSSs related to gene 2 chr1:30000-40000- (# nolint)
"chr1:29800-30000:-", # 3' convergent RNA.
"chr1:40101-40200:+", # uaRNA.
"chr1:40000-40099:+", # uaRNA overlaps with promoter.
"chr1:39901-40100:+", # aRNA overlaps with promoter.
"chr1:39801-40000:+", # daTSS that overlaps with promoter.
"chr1:39701-39900:-", # Alternative TSS at 100 bp.
"chr1:39701-39900:+", # daTSS at 100 bp.
"chr1:39601-39700:+", # daTSS at 300 bp.
"chr1:39401-39500:+" # daRNA at 500 bp.
))
S4Vectors::mcols(tss)$tss_id <- 1:length(tss)
idx_da_tss <- c(4, 6, 7, 13, 15, 16)
idx_ua_rna <- c(1, 10)
idx_enhancer <- c(1, 4)
dist_da_tss <- rep(c(0L, 100L, 300L), 2)
dist_ua_rna <- rep(100L, 2)
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