tests/testthat/test.computeRearrs.R
In dorolin/rearrvisr: Detect, Classify, and Visualize Genome Rearrangements
context("computeRearrs - main")
library(rearrvisr)
## computeRearrs<-function(focalgenome,compgenome,doubled,remWgt = 0.05,
## splitnodes = TRUE)
## test results
NM1<-rbind(0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0)
NM2<-rbind(0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0)
SM<-rbind(c(0.00, 0.00, 0.0),
c(0.95, 0.00, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.50, 0.0),
c(0.00, 0.00, 0.5),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(1.00, 0.00, 0.0))
IV<-rbind(0,
0,
0,
1,
1,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0)
nodeori<-rbind(c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, 9, NA),
c(NA, 9, NA, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 9))
blockori<-rbind(c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, -1, NA, NA),
c(NA, -1, NA, NA),
c(NA, -1, NA, NA),
c(NA, 9, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, 9, NA),
c(NA, 9, NA, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, 1, -1),
c(NA, 9, 1, -1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 9, 9))
blockid<-rbind(c(NA, "1", NA, NA),
c(NA, "4.1", NA, NA),
c(NA, "2.2", NA, NA),
c(NA, "3.2", NA, NA),
c(NA, "3.2", NA, NA),
c(NA, "3.2", NA, NA),
c(NA, "5", NA, NA),
c(NA, "1", NA, NA),
c(NA, "1", "1", NA),
c(NA, "1", NA, NA),
c(NA, "1", "1", NA),
c(NA, "1", "1", NA),
c(NA, "1", "1", NA),
c(NA, "1", NA, NA),
c(NA, "1", "0", NA),
c(NA, "1", "0", NA),
c(NA, "1", "0", NA),
c(NA, "1", "0", NA),
c(NA, "1", "2", "1.1"),
c(NA, "1", "2", "1.2"),
c(NA, "1", "2", "1"),
c(NA, "1", "2", "1"),
c(NA, "1", "2", "1"),
c(NA, "1", "1", "1"))
subnode<-rbind(c(0, 0, 0, 0),
c(0, 1, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(1, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 1),
c(0, 0, 0, 2),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 1, 0))
rownames(NM1)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(NM2)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(SM)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(IV)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(nodeori)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(blockori)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(blockid)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(subnode)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
## tests
test_that("function output of computeRearrs with test set TOY24", {
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$NM1, NM1)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$NM2, NM2)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$SM, SM)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$IV, IV)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$nodeori, nodeori)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$blockori, blockori)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$blockid, blockid)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$subnode, subnode)
})
dorolin/rearrvisr documentation built on Aug. 6, 2020, 1:32 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("computeRearrs - main")
library(rearrvisr)
## computeRearrs<-function(focalgenome,compgenome,doubled,remWgt = 0.05,
## splitnodes = TRUE)
## test results
NM1<-rbind(0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0)
NM2<-rbind(0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0)
SM<-rbind(c(0.00, 0.00, 0.0),
c(0.95, 0.00, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.05, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.50, 0.0),
c(0.00, 0.00, 0.5),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(0.00, 0.00, 0.0),
c(1.00, 0.00, 0.0))
IV<-rbind(0,
0,
0,
1,
1,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0)
nodeori<-rbind(c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, 9, NA),
c(NA, 9, NA, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 9))
blockori<-rbind(c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, -1, NA, NA),
c(NA, -1, NA, NA),
c(NA, -1, NA, NA),
c(NA, 9, NA, NA),
c(NA, 1, NA, NA),
c(NA, 1, 9, NA),
c(NA, 9, NA, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 1, -1, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, NA, NA),
c(NA, 9, 1, -1),
c(NA, 9, 1, -1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 1, 1),
c(NA, 9, 9, 9))
blockid<-rbind(c(NA, "1", NA, NA),
c(NA, "4.1", NA, NA),
c(NA, "2.2", NA, NA),
c(NA, "3.2", NA, NA),
c(NA, "3.2", NA, NA),
c(NA, "3.2", NA, NA),
c(NA, "5", NA, NA),
c(NA, "1", NA, NA),
c(NA, "1", "1", NA),
c(NA, "1", NA, NA),
c(NA, "1", "1", NA),
c(NA, "1", "1", NA),
c(NA, "1", "1", NA),
c(NA, "1", NA, NA),
c(NA, "1", "0", NA),
c(NA, "1", "0", NA),
c(NA, "1", "0", NA),
c(NA, "1", "0", NA),
c(NA, "1", "2", "1.1"),
c(NA, "1", "2", "1.2"),
c(NA, "1", "2", "1"),
c(NA, "1", "2", "1"),
c(NA, "1", "2", "1"),
c(NA, "1", "1", "1"))
subnode<-rbind(c(0, 0, 0, 0),
c(0, 1, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(1, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 1),
c(0, 0, 0, 2),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 0, 0),
c(0, 0, 1, 0))
rownames(NM1)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(NM2)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(SM)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(IV)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(nodeori)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(blockori)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(blockid)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
rownames(subnode)<-c("1","7","2","6","5","4","8","9","10","3","13","12","11",
"14","17","16","15","18","21","20","22","23","24","19")
## tests
test_that("function output of computeRearrs with test set TOY24", {
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$NM1, NM1)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$NM2, NM2)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$SM, SM)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$IV, IV)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$nodeori, nodeori)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$blockori, blockori)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$blockid, blockid)
expect_identical(computeRearrs(TOY24_focalgenome,TOY24_compgenome,
doubled = TRUE,remWgt = 0.05,
splitnodes = TRUE)$subnode, subnode)
})
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