testthat::context("Test alignment functions.")
test_findEqualGreater <- function() {
ret <- findEqualGreaterM(c(1,2,2,4), c(3))
testthat::expect_identical(ret,4)
}
test_align <- function() {
testthat::expect_error(align(NULL))
wrongMat1 <- matrix(0,ncol=2)
testthat::expect_error(align(wrongMat1))
wrongMat2 <- cbind(mz=c("21","22"),group=c(1,2))
testthat::expect_error(align(wrongMat2))
goodMat<- cbind(Mz=c(21.002,21.0021,21.0019),quanti=c(100,120,115),group=c(1,2,3))
res <- align(goodMat)
testthat::expect_equal(length(res),1)
testthat::expect_is(res,'list')
testthat::expect_equal(dim(res[[1]]),c(3,3))
}
test_alignSamples <- function(){
library(ptairData)
directory <- system.file("extdata/mycobacteria", package = "ptairData")
dirSet <- createPtrSet(directory, setName = "test", mzCalibRef =c(21.022,59.049))
dirSet <- detectPeak(dirSet, mzNominal = c(21,59),smoothPenalty = 0)
eset <- alignSamples(X = dirSet,quanti="ppb",pValGreaterThres = 1)
# output is expression set
testthat::expect_is(eset,'ExpressionSet')
#deux pics aligné
testthat::expect_equal(nrow(Biobase::exprs(eset)),2)
testthat::expect_equal(ncol(Biobase::exprs(eset)),6)
#test filer
eset <- alignSamples(dirSet,pValGreaterThres = 0.05)
testthat::expect_equal(ncol(Biobase::fData(eset)),7)
testthat::expect_equal(nrow(Biobase::exprs(eset)),1)
}
test_impute<-function(){
library(ptairData)
directory <- system.file("extdata/mycobacteria", package = "ptairData")
dirSet <- createPtrSet(directory, setName = "test", mzCalibRef =c(21.022,59.049))
dirSet <- detectPeak(dirSet,mz=c(21,63,77),minIntensity =50,smoothPenalty = 0)
eset <- alignSamples(dirSet, pValGreaterThres = 1,fracGroup = 0,bgCorrected =FALSE)
testthat::expect_equal(sum(is.na(Biobase::exprs(eset))),3)
X<-Biobase::exprs(eset)
eset<-impute(eset,dirSet)
Ximpute<-Biobase::exprs(eset)
testthat::expect_equal(sum(is.na(Biobase::exprs(eset))),0)
testthat::expect_true(round(Ximpute[2,1],2)<1)
}
testthat::test_that("findEqualGreater() works correctly.", test_findEqualGreater())
testthat::test_that("align() works correctly.", test_align())
testthat::test_that("alignSamples() works correctly.", test_alignSamples())
testthat::test_that("impute() works correctly.", test_impute())
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