examples/example-colstats.R

In privefl/bigstatsr: Statistical Tools for Filebacked Big Matrices

set.seed(1)

X <- big_attachExtdata()

# Check the results
str(test <- big_colstats(X))

# Only with the first 100 rows
ind <- 1:100
str(test2 <- big_colstats(X, ind.row = ind))
plot(test$sum, test2$sum)
abline(lm(test2$sum ~ test$sum), col = "red", lwd = 2)

X.ind <- X[ind, ]
all.equal(test2$sum, colSums(X.ind))
all.equal(test2$var, apply(X.ind, 2, var))

# deduce mean and sd
# note that the are also implemented in big_scale()
means <- test2$sum / length(ind) # if using all rows,
                                 # divide by nrow(X) instead
all.equal(means, colMeans(X.ind))
sds <- sqrt(test2$var)
all.equal(sds, apply(X.ind, 2, sd))