examples/example-apply.R

In privefl/bigstatsr: Statistical Tools for Filebacked Big Matrices

X <- big_attachExtdata()

# get the means of each column
colMeans_sub <- function(X, ind) colMeans(X[, ind])
str(colmeans <- big_apply(X, a.FUN = colMeans_sub, a.combine = 'c'))

# get the norms of each column
colNorms_sub <- function(X, ind) sqrt(colSums(X[, ind]^2))
str(colnorms <- big_apply(X, colNorms_sub, a.combine = 'c'))

# get the sums of each row
# split along rows: need to change the "complete" `ind` parameter
str(rowsums <- big_apply(X, a.FUN = function(X, ind) rowSums(X[ind, ]),
                         ind = rows_along(X), a.combine = 'c',
                         block.size = 100))
# it is usually preferred to split along columns
# because matrices are stored by column.
str(rowsums2 <- big_apply(X, a.FUN = function(X, ind) rowSums(X[, ind]),
                          a.combine = 'plus'))