context("scan_motifs")
data("scan_interactions_example", package = "spatzie")
test_that("can scan motifs with motifmatchr", {
motifs_file <- system.file("extdata/motifs_subset.txt.gz",
package = "spatzie")
motifs <- TFBSTools::readJASPARMatrix(motifs_file, matrixClass = "PFM")
left <- GenomicRanges::GRanges(
seqnames = c("chr1", "chr1", "chr1"),
ranges = IRanges::IRanges(start = c(1, 15, 20),
end = c(10, 35, 31)))
right <- GenomicRanges::GRanges(
seqnames = c("chr1", "chr2", "chr2"),
ranges = IRanges::IRanges(start = c(17, 47, 41),
end = c(28, 54, 53)))
test_interactions <- GenomicInteractions::GenomicInteractions(left, right)
# toy DNAStringSet to replace BSgenome object
seqs <- c("chr1" = "CCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCC",
"chr2" = "CTACAAACTAGGAATTTAGGCAAACCTGTGTTAAAATCTTAGCTCATTCATTAAT")
toy_genome <- Biostrings::DNAStringSet(seqs, use.names = TRUE)
scanned_interactions <- scan_motifs(test_interactions, motifs, toy_genome)
expect_is(scanned_interactions, "interactionData")
expect_is(scanned_interactions$anchor1_motifs, "RangedSummarizedExperiment")
expect_is(scanned_interactions$anchor2_motifs, "RangedSummarizedExperiment")
})
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