bigpca (version 1.1)

generate.test.matrix: Generate a test matrix of random data

Description

Generates a test matrix of easily specified size and type. Options allow automated row and column names (which might resemble labels for a SNP analysis) and return of several different formats, matrix, data.frame or big.matrix. You can specify the randomisation function (e.g, rnorm, runif, etc), as well as parameters determining the matrix size. Can also generate big.matrix objects, and an important feature is that the method to generate big.matrix objects is scalable so that very large matrices for simulation can be generated only limited by disk space and not by RAM.

Usage

generate.test.matrix(size = 5, row.exp = 2, rand = rnorm,
  dimnames = TRUE, data.frame = FALSE, big.matrix = FALSE,
  file.name = NULL, tracker = TRUE)

Arguments

size

10^size is the total number of datapoints simulated. 6 or less are fairly quick to generate, while 7 takes a few seconds. 8 will take under a minute, 9 around ten minutes, 10, perhaps over an hour. Values are coerced to the range of integers c(2:10).

row.exp

similar to 'nrow' when creating a matrix, except this is exponential, giving 10^row.exp rows.

rand

a function, must return 'n' values, when rand(n) is called, eg., rnorm(), runif(), numeric()

dimnames

logical, whether to generate some row and column names

data.frame

logical, whether to return as a data.frame (FALSE means return a matrix)

big.matrix

logical, whether to return as a big.matrix (overrides data.frame). If a file.name is used then the big.matrix will be filebacked and this function returns a list with a a big.matrix, and the description and backing filenames.

file.name

if a character, then will write the result to tab file instead of returning the object, will return the filename; overrides data.frame. Alternatively, if big.matrix=TRUE, then this provides the basename for a filebacked big.matrix.

tracker

logical, whether to display a progress bar for large matrices (size>7) where progress will be slow

Value

Returns a random matrix of data for testing/simulation, can be a data.frame or big.matrix if those options are selected

Examples

# NOT RUN {
orig.dir <- getwd(); setwd(tempdir()); # move to temporary dir
mat <- (generate.test.matrix(5)); prv(mat)
lst <- (generate.test.matrix(5,3,big.matrix=TRUE,file.name="bigtest"))
mat <- lst[[1]]; prv(mat); headl(lst[2:3]); 
unlink(unlist(lst[2:3]))
setwd(orig.dir) # reset working dir to original
# }