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bigcorPar <- function(x, nblocks = 10, verbose = TRUE, ncore="all", ...){ | |
library(ff, quietly = TRUE) | |
require(doMC) | |
if(ncore=="all"){ | |
ncore = multicore:::detectCores() | |
registerDoMC(cores = ncore) | |
} else{ | |
registerDoMC(cores = ncore) | |
} | |
NCOL <- ncol(x) | |
## test if ncol(x) %% nblocks gives remainder 0 | |
if (NCOL %% nblocks != 0){stop("Choose different 'nblocks' so that ncol(x) %% nblocks = 0!")} | |
## preallocate square matrix of dimension | |
## ncol(x) in 'ff' single format | |
corMAT <- ff(vmode = "single", dim = c(NCOL, NCOL)) | |
## split column numbers into 'nblocks' groups | |
SPLIT <- split(1:NCOL, rep(1:nblocks, each = NCOL/nblocks)) | |
## create all unique combinations of blocks | |
COMBS <- expand.grid(1:length(SPLIT), 1:length(SPLIT)) | |
COMBS <- t(apply(COMBS, 1, sort)) | |
COMBS <- unique(COMBS) | |
## iterate through each block combination, calculate correlation matrix | |
## between blocks and store them in the preallocated matrix on both | |
## symmetric sides of the diagonal | |
results <- foreach(i = 1:nrow(COMBS)) %dopar% { | |
COMB <- COMBS[i, ] | |
G1 <- SPLIT[[COMB[1]]] | |
G2 <- SPLIT[[COMB[2]]] | |
if (verbose) cat("Block", COMB[1], "with Block", COMB[2], "\n") | |
flush.console() | |
COR <- cor(x[, G1], x[, G2], ...) | |
corMAT[G1, G2] <- COR | |
corMAT[G2, G1] <- t(COR) | |
COR <- NULL | |
} | |
gc() | |
return(corMAT) | |
} |
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