gdsfmt
R Interface to CoreArray Genomic Data Structure (GDS) Files

Package index
Search the gdsfmt package
Vignettes
Functions
111
Source code
15
Man pages
46
Home
/
Bioconductor
/
gdsfmt
/
inst/unitTests/test_07_randomaccess.R

inst/unitTests/test_07_randomaccess.R
In gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files 

#############################################################
#
# DESCRIPTION: test data dimension
#

library(RUnit)
library(gdsfmt)


#############################################################
#
# test functions
#

test.random_access_1 <- function()
{
	on.exit({
		showfile.gds(closeall=TRUE, verbose=FALSE)
		unlink("tmp.gds", force=TRUE)
	})

	verbose <- options("test.verbose")$test.verbose
	if (verbose) cat("\n>>>> test.random_access_1 <<<<\n")

	########  High Compression Rate (ratio: 6.3%)  ########

	####  cteate a GDS file  ####
	f <- createfn.gds("tmp.gds")

	set.seed(1000)
	v <- as.integer(rnorm(1000000) >= 0)

	n0 <- add.gdsn(f, "I0", val=v, compress="")
	readmode.gdsn(n0)

	n1 <- add.gdsn(f, "I1", val=v, compress="ZIP")
	readmode.gdsn(n1)

	n2 <- add.gdsn(f, "I2", val=v, compress="ZIP_RA:16K")
	readmode.gdsn(n2)

	closefn.gds(f)


	####  open the GDS file  ####
	f <- openfn.gds("tmp.gds")

	n0 <- index.gdsn(f, "I0")
	n1 <- index.gdsn(f, "I1")
	n2 <- index.gdsn(f, "I2")

	z0 <- read.gdsn(n0)
	z1 <- read.gdsn(n1)
	z2 <- read.gdsn(n2)
	checkEquals(z0, z1, "random access, all together [z0==z1]")
	checkEquals(z0, z2, "random access, all together [z0==z2]")

	set.seed(1000)
	for (k in 1:10)
	{
		idx <- sample.int(length(v), 100)

		v0 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v0[i] <- read.gdsn(n0, start=idx[i], count=1)

		v1 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v1[i] <- read.gdsn(n1, start=idx[i], count=1)

		v2 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v2[i] <- read.gdsn(n2, start=idx[i], count=1)

		vv <- v[idx]
		checkEquals(v0, vv, sprintf("random access (%d), all together [v0]", k))
		checkEquals(v1, vv, sprintf("random access (%d), all together [v1]", k))
		checkEquals(v2, vv, sprintf("random access (%d), all together [v2]", k))
	}

	# close the file
	closefn.gds(f)
}


test.random_access_2 <- function()
{
	on.exit({
		showfile.gds(closeall=TRUE, verbose=FALSE)
		unlink("tmp.gds", force=TRUE)
	})

	verbose <- options("test.verbose")$test.verbose
	if (verbose) cat("\n>>>> test.random_access_2 <<<<\n")

	########  Low Compression Rate (ratio: 85.5%)  ########

	####  cteate a GDS file  ####
	f <- createfn.gds("tmp.gds")

	set.seed(1000)
	v <- as.integer(rnorm(1000000) * 2^20)

	n0 <- add.gdsn(f, "I0", val=v, compress="")
	readmode.gdsn(n0)

	n1 <- add.gdsn(f, "I1", val=v, compress="ZIP")
	readmode.gdsn(n1)

	n2 <- add.gdsn(f, "I2", val=v, compress="ZIP_RA:16K")
	readmode.gdsn(n2)

	closefn.gds(f)


	####  open the GDS file  ####
	f <- openfn.gds("tmp.gds")

	n0 <- index.gdsn(f, "I0")
	n1 <- index.gdsn(f, "I1")
	n2 <- index.gdsn(f, "I2")

	z0 <- read.gdsn(n0)
	z1 <- read.gdsn(n1)
	z2 <- read.gdsn(n2)
	checkEquals(z0, z1, "random access, all together [z0==z1]")
	checkEquals(z0, z2, "random access, all together [z0==z2]")

	set.seed(1000)
	for (k in 1:10)
	{
		idx <- sample.int(length(v), 100)

		v0 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v0[i] <- read.gdsn(n0, start=idx[i], count=1)

		v1 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v1[i] <- read.gdsn(n1, start=idx[i], count=1)

		v2 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v2[i] <- read.gdsn(n2, start=idx[i], count=1)

		vv <- v[idx]
		checkEquals(v0, vv, sprintf("random access (%d), all together [v0]", k))
		checkEquals(v1, vv, sprintf("random access (%d), all together [v1]", k))
		checkEquals(v2, vv, sprintf("random access (%d), all together [v2]", k))
	}

	# close the file
	closefn.gds(f)
}


test.random_access_bit1 <- function()
{
	on.exit({
		showfile.gds(closeall=TRUE, verbose=FALSE)
		unlink("tmp.gds", force=TRUE)
	})

	verbose <- options("test.verbose")$test.verbose
	if (verbose) cat("\n>>>> test.random_access_bit1 <<<<\n")

	########  Unable to compress (ratio: >100%)  ########

	####  cteate a GDS file  ####
	f <- createfn.gds("tmp.gds")

	set.seed(1000)
	v <- as.integer(rnorm(1000000) >= 0)

	n0 <- add.gdsn(f, "I0", val=v, storage="bit1", compress="")
	readmode.gdsn(n0)

	n1 <- add.gdsn(f, "I1", val=v, storage="bit1", compress="ZIP")
	readmode.gdsn(n1)

	n2 <- add.gdsn(f, "I2", val=v, storage="bit1", compress="ZIP_RA:16K")
	readmode.gdsn(n2)

	closefn.gds(f)


	####  open the GDS file  ####
	f <- openfn.gds("tmp.gds")

	n0 <- index.gdsn(f, "I0")
	n1 <- index.gdsn(f, "I1")
	n2 <- index.gdsn(f, "I2")

	z0 <- read.gdsn(n0)
	z1 <- read.gdsn(n1)
	z2 <- read.gdsn(n2)
	checkEquals(z0, z1, "random access, all together [z0==z1]")
	checkEquals(z0, z2, "random access, all together [z0==z2]")

	set.seed(1000)
	for (k in 1:10)
	{
		idx <- sample.int(length(v), 5000)

		v0 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v0[i] <- read.gdsn(n0, start=idx[i], count=1)

		v1 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v1[i] <- read.gdsn(n1, start=idx[i], count=1)

		v2 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v2[i] <- read.gdsn(n2, start=idx[i], count=1)

		vv <- v[idx]
		checkEquals(v0, vv, sprintf("random access (%d), all together [v0]", k))
		checkEquals(v1, vv, sprintf("random access (%d), all together [v1]", k))
		checkEquals(v2, vv, sprintf("random access (%d), all together [v2]", k))
	}

	# close the file
	closefn.gds(f)
}


test.random_access_bit2 <- function()
{
	on.exit({
		showfile.gds(closeall=TRUE, verbose=FALSE)
		unlink("tmp.gds", force=TRUE)
	})

	verbose <- options("test.verbose")$test.verbose
	if (verbose) cat("\n>>>> test.random_access_bit2 <<<<\n")

	########  Median Compression Rate (ratio: ~56%)  ########

	####  cteate a GDS file  ####
	f <- createfn.gds("tmp.gds")

	set.seed(1000)
	v <- as.integer(sample(0:3, 1000000, TRUE))

	n0 <- add.gdsn(f, "I0", val=v, storage="bit2", compress="")
	readmode.gdsn(n0)

	n1 <- add.gdsn(f, "I1", val=v, storage="bit2", compress="ZIP")
	readmode.gdsn(n1)

	n2 <- add.gdsn(f, "I2", val=v, storage="bit2", compress="ZIP_RA:16K")
	readmode.gdsn(n2)

	closefn.gds(f)


	####  open the GDS file  ####
	f <- openfn.gds("tmp.gds")

	n0 <- index.gdsn(f, "I0")
	n1 <- index.gdsn(f, "I1")
	n2 <- index.gdsn(f, "I2")

	z0 <- read.gdsn(n0)
	z1 <- read.gdsn(n1)
	z2 <- read.gdsn(n2)
	checkEquals(z0, z1, "random access, all together [z0==z1]")
	checkEquals(z0, z2, "random access, all together [z0==z2]")

	set.seed(1000)
	for (k in 1:10)
	{
		idx <- sample.int(length(v), 5000)

		v0 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v0[i] <- read.gdsn(n0, start=idx[i], count=1)

		v1 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v1[i] <- read.gdsn(n1, start=idx[i], count=1)

		v2 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v2[i] <- read.gdsn(n2, start=idx[i], count=1)

		vv <- v[idx]
		checkEquals(v0, vv, sprintf("random access (%d), all together [v0]", k))
		checkEquals(v1, vv, sprintf("random access (%d), all together [v1]", k))
		checkEquals(v2, vv, sprintf("random access (%d), all together [v2]", k))
	}

	# close the file
	closefn.gds(f)
}


test.random_access_bit4 <- function()
{
	on.exit({
		showfile.gds(closeall=TRUE, verbose=FALSE)
		unlink("tmp.gds", force=TRUE)
	})

	verbose <- options("test.verbose")$test.verbose
	if (verbose) cat("\n>>>> test.random_access_bit4 <<<<\n")

	########  Median Compression Rate (ratio: ~56%)  ########

	####  cteate a GDS file  ####
	f <- createfn.gds("tmp.gds")

	set.seed(1000)
	v <- as.integer(sample(0:15, 1000000, TRUE))

	n0 <- add.gdsn(f, "I0", val=v, storage="bit4", compress="")
	readmode.gdsn(n0)

	n1 <- add.gdsn(f, "I1", val=v, storage="bit4", compress="ZIP")
	readmode.gdsn(n1)

	n2 <- add.gdsn(f, "I2", val=v, storage="bit4", compress="ZIP_RA:16K")
	readmode.gdsn(n2)

	closefn.gds(f)


	####  open the GDS file  ####
	f <- openfn.gds("tmp.gds")

	n0 <- index.gdsn(f, "I0")
	n1 <- index.gdsn(f, "I1")
	n2 <- index.gdsn(f, "I2")

	z0 <- read.gdsn(n0)
	z1 <- read.gdsn(n1)
	z2 <- read.gdsn(n2)
	checkEquals(z0, z1, "random access, all together [z0==z1]")
	checkEquals(z0, z2, "random access, all together [z0==z2]")

	set.seed(1000)
	for (k in 1:10)
	{
		idx <- sample.int(length(v), 5000)

		v0 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v0[i] <- read.gdsn(n0, start=idx[i], count=1)

		v1 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v1[i] <- read.gdsn(n1, start=idx[i], count=1)

		v2 <- rep.int(0, length(idx))
		for (i in 1:length(idx))
			v2[i] <- read.gdsn(n2, start=idx[i], count=1)

		vv <- v[idx]
		checkEquals(v0, vv, sprintf("random access (%d), all together [v0]", k))
		checkEquals(v1, vv, sprintf("random access (%d), all together [v1]", k))
		checkEquals(v2, vv, sprintf("random access (%d), all together [v2]", k))
	}

	# close the file
	closefn.gds(f)
}


test.random_access_sparse <- function()
{
	on.exit({
		showfile.gds(closeall=TRUE, verbose=FALSE)
		unlink("tmp.gds", force=TRUE)
	})

	verbose <- options("test.verbose")$test.verbose
	if (verbose) cat("\n>>>> test.random_access_sparse <<<<\n")

	########  Median Compression Rate (ratio: ~56%)  ########

	####  cteate a GDS file  ####
	f <- createfn.gds("tmp.gds")

	set.seed(1000)
	N <- 2000
	mat <- matrix(sample.int(2, N*N, replace=TRUE, prob=c(0.95, 0.05))-1L,
		nrow=N)
	mat[mat==1] <- seq_len(sum(mat))
	add.gdsn(f, "mat", val=mat, storage="sp.real")
	closefn.gds(f)


	####  open the GDS file  ####
	f <- openfn.gds("tmp.gds")

	n1 <- index.gdsn(f, "mat")
	z1 <- read.gdsn(n1, .sparse=FALSE)
	z2 <- read.gdsn(n1, .sparse=TRUE)
	checkEquals(mat, z1, "sparse access, all [z1]")
	checkEquals(Matrix(mat, sparse=TRUE), z2, "sparse access, all [z2]")

	set.seed(1000)
	M <- 100
	for (k in 1:10)
	{
		i <- sample.int(N-2*M, 2, replace=TRUE)
		m0 <- mat[seq(i[1], length.out=M), seq(i[2], length.out=2*M)]
		z1 <- read.gdsn(n1, start=i, count=c(M, 2*M), .sparse=FALSE)
		z2 <- read.gdsn(n1, start=i, count=c(M, 2*M), .sparse=TRUE)
		checkEquals(m0, z1, sprintf("sparse random access (z1 %d)", k))
		checkEquals(Matrix(m0, sparse=TRUE), z2, sprintf("sparse random access (z2 %d)", k))
	}

	for (k in 1:10)
	{
		i <- sample.int(4L, N, replace=TRUE)==1L
		j <- sample.int(4L, N, replace=TRUE)==2L
		m0 <- mat[i, j]
		z1 <- readex.gdsn(n1, list(i, j), .sparse=FALSE)
		z2 <- readex.gdsn(n1, list(i, j), .sparse=TRUE)
		checkEquals(m0, z1, sprintf("sparse random access ex (z1 %d)", k))
		checkEquals(Matrix(m0, sparse=TRUE), z2, sprintf("sparse random access ex (z2 %d)", k))
	}

	# close the file
	closefn.gds(f)
}

Try the gdsfmt package in your browser

Any scripts or data that you put into this service are public.

gdsfmt documentation built on Dec. 26, 2020, 6 p.m.

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close