making smaller gwama files

smaller_gwama.r

1M = 16mb

a <- read.table('results_9.gz', he=T)

snplist <- as.character(unique(a$SNP))
snplist <- data.frame(SNP=snplist, snpid=1:length(snplist), stringsAsFactors=FALSE)

cpglist <- as.character(unique(a$PHENOTYPE))
cpglist <- data.frame(CPG=cpglist, cpgid=1:length(cpglist), stringsAsFactors=FALSE)

a$cpgid <- cpglist$cpgid[match(a$PHENOTYPE, cpglist$CPG)]
a$snpid <- snplist$snpid[match(a$SNP, snplist$SNP)]


writebin <- function(a, filename="test")
{
	unlink(filename)
	zz <- file(filename, "wb")
	writeBin(as.integer(nrow(a)), con=zz)
	writeBin(as.integer(a$snpid), con=zz)
	writeBin(as.integer(a$cpgid), con=zz)
	writeBin(as.character(a$CISTRANS), con=zz)
	writeBin(as.numeric(a$BETA), con=zz)
	writeBin(as.numeric(a$SE), con=zz)
	writeBin(as.numeric(a$PVAL), con=zz)
	writeBin(as.integer(a$N), con=zz)
	writeBin(as.character(a$EA), con=zz)
	writeBin(as.character(a$NEA), con=zz)
	writeBin(as.numeric(a$EAF), con=zz)
	close(zz)
}

readbin <- function(filename="test")
{
	zz <- file(filename, "rb")
	n <- readBin(zz, integer(), 1)
	snpid <- readBin(zz, integer(), n)
	cpgid <- readBin(zz, integer(), n)
	cistrans <- readBin(zz, character(), n)
	beta <- readBin(zz, numeric(), n)
	se <- readBin(zz, numeric(), n)
	pval <- readBin(zz, numeric(), n)
	n <- readBin(zz, integer(), n)
	ea <- readBin(zz, character(), n)
	nea <- readBin(zz, character(), n)
	eaf <- readBin(zz, numeric(), n)
	close(zz)
}


b <- subset(a, select=c(cpgid, snpid, CISTRANS, BETA, SE, PVAL, N, EA, NEA, EAF))

c <- subset(a, select=c(CISTRANS, BETA, SE, PVAL, N, EA, NEA, EAF))
c$MARKERNAME <- paste0(a$cpgid, "_", a$snpid)
write.table(c, file="test3.txt", row=F, col=T, qu=F)


zz <- file("testbin", "wb")
writeBin(pi, zz)
writeBin(pi, zz)
writeBin(pi, zz, endian = "swap")
writeBin(pi, zz, size = 4)
writeBin(pi^2, zz, size = 4, endian = "swap")
writeBin(pi+3i, zz)
writeBin("A test of a connection", zz)
z <- paste("A very long string", 1:100, collapse = " + ")
writeBin(z, zz)
if(.Machine$sizeof.long == 8 || .Machine$sizeof.longlong == 8)
writeBin(as.integer(5^(1:10)), zz, size = 8)
if((s <- .Machine$sizeof.longdouble) > 8)
writeBin((pi/3)^(1:10), zz, size = s)
close(zz)

zz <- file("testbin", "rb")
readBin(zz, character(), 4)
readBin(zz, integer(), 6)
readBin(zz, numeric(), 1, endian = "swap")
readBin(zz, numeric(), size = 4)
readBin(zz, numeric(), size = 4, endian = "swap")
readBin(zz, complex(), 1)
readBin(zz, character(), 1)
z2 <- readBin(zz, character(), 1)
if(.Machine$sizeof.long == 8 || .Machine$sizeof.longlong == 8)
readBin(zz, integer(), 10,  size = 8)
if((s <- .Machine$sizeof.longdouble) > 8)
readBin(zz, numeric(), 10, size = s)
close(zz)
unlink("testbin")