tests/testthat/helper-granges.R

In coregenomics/nascentrna: Classify Nascent RNA Transcripts using Decision Tree

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)