Nothing
################
# Test mpp_CIM #
################
context("Test mpp_CIM")
# library(testthat)
# library(mppR)
# references values (taken on the USNAM example - 24/05/2019)
ref_ind <- c(8, 9, 11, 20, 24, 32, 37, 57, 68, 94)
ref_ind2 <- c(43, 74)
# reference -log10(p-valu)
logp_cr <- c(1.10021694, 1.68789781, 3.59980702, 0.22957343, 3.69385531,
0.02685481, 1.43415436, 3.66469958, 1.16856072, 0.52939162)
logp_par <- c(1.10021694, 1.68789781, 3.59980702, 0.22957343, 3.69385531,
0.02685481, 1.43415436, 3.66469958, 1.16856072, 0.52939162)
logp_anc <- c(1.3194567, 2.3176857, 4.2831107, 0.4738949, 3.6928160,
0.1501479, 1.8364183, 4.0360087, 1.4299513, 0.6208097)
logp_biall <- c(1.90194112, 2.00673871, 2.30011066, 1.71703106, 2.19542051,
0.40400271, 1.12271256, 0.21386840, 0.43960028, 0.01652987)
Ref_logp <- cbind(logp_cr, logp_par, logp_anc, logp_biall)
# reference QTL allele p-val
pval_cr <- c(0.05659636, 0.66696803, 0.75184962, 0.31062668, 0.63682840,
0.26334557, -0.29658559, -0.35759213, 0.02310737, 0.04511828)
pval_par <- c(1.00000000, 1.00000000, 0.05659636, 0.66696803, 0.75184962,
0.31062668, 0.63682840, 0.26334557, -0.29658559, -0.35759213,
0.02310737, 0.04511828)
pval_anc <- c(1.00000000, 1.00000000, 0.09159886, 0.30683944, 0.75371835,
0.30683944, 0.62045555, 0.91931724, 0.09159886, 0.91931724,
0.09159886, 0.04863690)
Ref_pval <- list(pval_cr, pval_par, pval_anc)
data(mppData)
Qeff <- c('cr', 'par', 'anc', 'biall')
for(i in 1:4){
CIM <- mpp_CIM(mppData = mppData, Q.eff = Qeff[i],
cofactors = c('L00585', 'L00194'),
plot.gen.eff = Qeff[i]!='biall')
test_i <- paste('Q.eff =', Qeff[i])
test_that(test_i, {
expect_equal(object = CIM$log10pval[ref_ind], expected = Ref_logp[, i],
tolerance = .001)
})
if(Qeff[i]!='biall'){
test_i <- paste0('Q_pval_', Qeff[i])
test_that(test_i, {
pval_i <- unlist(CIM[ref_ind2, 6:dim(CIM)[2]])
names(pval_i) <- NULL
expect_equal(object = pval_i, expected = Ref_pval[[i]], tolerance = .001)
})
}
}
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