Nothing
context("Mutations")
library("SynMut")
filepath <- system.file("extdata", "example.fasta", package = "SynMut")
filepath.csv <- system.file("extdata", "target_regions.csv", package = "SynMut")
region <- read.csv(filepath.csv)
rgd.seq <- input_seq(filepath, region)
rgd.seq.no.region <- input_seq(filepath)
filepath <-
system.file("extdata", "example2.fasta", package = "SynMut")
rgd.seq.single <- input_seq(filepath)
test_that("codon_random", {
expect_silent(seq_random(n = 1, m = 99))
expect_silent(seq_random(n = 10, m = 30))
expect_silent(seq_random(n = 10, m = 1:10))
expect_silent(seq_random(
n = 10,
m = 100,
no.stop.codon = TRUE
))
})
test_that("codon_random", {
tmp <- codon_random(rgd.seq, n = 0.5)
expect_true(class(tmp)[1] == "regioned_dna")
expect_silent(codon_random(rgd.seq.single, n = 0.5))
expect_silent(codon_random(rgd.seq.no.region, n = 0.5))
})
test_that("codon_to", {
expect_error(codon_to(rgd.seq, max.codon = "aac", min.codon = "aac"))
expect_error(codon_to(rgd.seq))
expect_error(codon_to(rgd.seq, min.codon = "aaaa"))
tmp <-
get_cu(codon_to(rgd.seq, max.codon = "AAC")) - get_cu(rgd.seq)
expect_true(class(tmp)[1] == "matrix")
expect_silent(codon_to(rgd.seq.single, min.codon = "aaa"))
expect_silent(codon_to(rgd.seq.no.region, min.codon = "aaa"))
})
test_that("dinu_to", {
tmp <- dinu_to(rgd.seq, max.dinu = "cg")
expect_true(class(tmp)[1] == "regioned_dna")
tmp <- get_du(dinu_to(rgd.seq, min.dinu = "aa")) - get_du(rgd.seq)
expect_true(class(tmp)[1] == "matrix")
expect_silent(dinu_to(rgd.seq.single, max.dinu = "cg"))
expect_silent(dinu_to(rgd.seq.no.region, max.dinu = "cg"))
expect_silent(get_du(dinu_to(
rgd.seq, max.dinu = "cg", keep = TRUE
)))
expect_silent(get_du(dinu_to(
rgd.seq, min.dinu = "tg", keep = TRUE
)))
expect_silent(get_cu(dinu_to(
rgd.seq.single, max.dinu = "cg", keep = TRUE
)))
expect_silent(get_du(dinu_to(
rgd.seq.single, min.dinu = "tg", keep = TRUE
)))
expect_silent(get_cu(dinu_to(
rgd.seq.no.region, max.dinu = "cg", keep = TRUE
)))
expect_silent(get_du(dinu_to(
rgd.seq.no.region, min.dinu = "tg", keep = TRUE
)))
})
test_that("codon_mimic", {
target <- get_cu(rgd.seq)[2,]
new <- codon_mimic(rgd.seq, alt = target)
tmp <- get_freq(new) - get_freq(rgd.seq)
expect_true(class(tmp)[1] == "matrix")
target <- Biostrings::DNAStringSet("TTGAAAA-CTC-N--AAG")
new <- codon_mimic(rgd.seq, alt = target)
tmp <- get_cu(new) - get_cu(rgd.seq)
expect_true(class(tmp)[1] == "matrix")
expect_silent(codon_mimic(rgd.seq.single, alt = target))
expect_silent(codon_mimic(rgd.seq.no.region, alt = target))
})
test_that("dinu_dist", {
expect_silent(codon_dist(codon_random(rgd.seq), rgd.seq))
expect_silent(dinu_dist(codon_random(rgd.seq), rgd.seq))
})
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