source("R/utils.R")
Rcpp::sourceCpp('src/pruning.cpp')
lims <- c(1, ncol(X))
S <- maf$S
exclude <- sample(ncol(X), size = 50)
size <- 500
X.chr <- X
ind.train <- seq(nrow(X.chr))
thr.corr <- 0.01
ind.chr <- seq2(lims)
m.chr <- length(ind.chr)
S.chr <- S[ind.chr]
ord.chr <- order(S.chr, decreasing = TRUE)
size <- min(size, m.chr)
s <- setdiff(-size:size, 0)
# init
keep <- rep(FALSE, m.chr)
remain <- rep(TRUE, m.chr)
remain[exclude] <- FALSE
for (ind in ord.chr) {
if (remain[ind]) { # already excluded?
ind.col <- intersect(ind + s, which(remain))
res <- R_squared_chr(pBigMat = X.chr@address,
rowInd = ind.train,
colInd = ind.col,
colMat0 = X.chr[, ind])
remain[ind.col[res > thr.corr]] <- FALSE
keep[ind] <- TRUE
}
}
ind.chr[keep]
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