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test_that("test_PFMSimilarity", {
library(Biostrings)
skip_if_not_installed("JASPAR2016")
library(JASPAR2016)
profileMatrix <- matrix(as.integer(
c(13, 13, 3, 1, 54, 1, 1, 1, 0, 3, 2, 5,
13, 39, 5, 53, 0, 1, 50, 1, 0, 37, 0, 17,
17, 2, 37, 0, 0, 52, 3, 0, 53, 8, 37, 12,
11, 0, 9, 0, 0, 0, 0, 52, 1, 6, 15, 20)),
nrow=4, byrow=TRUE, dimnames=list(DNA_BASES))
pfmQuery <- PFMatrix(profileMatrix=profileMatrix)
pfmSubjects <- getMatrixSet(JASPAR2016,
opts=list(ID=c("MA0500", "MA0499", "MA0521",
"MA0697")))
scores <- PFMSimilarity(pfmSubjects, pfmQuery)
expect_equal(unname(scores[[1]]), c(20.65002, 93.86375), tolerance=0.01)
expect_equal(unname(scores[[2]]), c(20.52325, 85.51356), tolerance=0.01)
expect_equal(unname(scores[[3]]), c(20.44110, 92.91409), tolerance=0.01)
expect_equal(unname(scores[[4]]), c(20.04603, 83.52514), tolerance=0.01)
}
)
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