examples/example-univLogReg.R

In privefl/bigstatsr: Statistical Tools for Filebacked Big Matrices

set.seed(1)

X <- big_attachExtdata()
n <- nrow(X)
y01 <- sample(0:1, size = n, replace = TRUE)
covar <- matrix(rnorm(n * 3), n)

X1 <- X[, 1] # only first column of the Filebacked Big Matrix

# Without covar
test <- big_univLogReg(X, y01)
## new class `mhtest`
class(test)
attr(test, "transfo")
attr(test, "predict")
## plot results
plot(test)
plot(test, type = "Volcano")
## To get p-values associated with the test
test$p.value <- predict(test, log10 = FALSE)
str(test)
summary(glm(y01 ~ X1, family = "binomial"))$coefficients[2, ]

# With all data
str(big_univLogReg(X, y01, covar.train = covar))
summary(glm(y01 ~ X1 + covar, family = "binomial"))$coefficients[2, ]

# With only half of the data
ind.train <- sort(sample(n, n/2))
str(big_univLogReg(X, y01[ind.train],
                   covar.train = covar[ind.train, ],
                   ind.train = ind.train))
summary(glm(y01 ~ X1 + covar, family = "binomial",
            subset = ind.train))$coefficients[2, ]