biglasso: setupX – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

setupX

Set up design matrix X by reading data from big data file

Description

Set up the design matrix X as a big.matrix object based on external massive data file stored on disk that cannot be fullly loaded into memory. The data file must be a well-formated ASCII-file, and contains only one single type. Current version only supports double type. Other restrictions about the data file are described in biglasso-package. This function reads the massive data, and creates a big.matrix object. By default, the resulting big.matrix is file-backed, and can be shared across processors or nodes of a cluster.

Usage

setupX(
  filename,
  dir = getwd(),
  sep = ",",
  backingfile = paste0(unlist(strsplit(filename, split = "\\."))[1], ".bin"),
  descriptorfile = paste0(unlist(strsplit(filename, split = "\\."))[1], ".desc"),
  type = "double",
  ...
)

Arguments

`filename`	The name of the data file. For example, "dat.txt".
`dir`	The directory used to store the binary and descriptor files associated with the `big.matrix`. The default is current working directory.
`sep`	The field separator character. For example, "," for comma-delimited files (the default); "\t" for tab-delimited files.
`backingfile`	The binary file associated with the file-backed `big.matrix`. By default, its name is the same as `filename` with the extension replaced by ".bin".
`descriptorfile`	The descriptor file used for the description of the file-backed `big.matrix`. By default, its name is the same as `filename` with the extension replaced by ".desc".
`type`	The data type. Only "double" is supported for now.
`...`	Additional arguments that can be passed into function `read.big.matrix`.

Details

For a data set, this function needs to be called only one time to set up the big.matrix object with two backing files (.bin, .desc) created in current working directory. Once set up, the data can be "loaded" into any (new) R session by calling attach.big.matrix(discriptorfile).

This function is a simple wrapper of read.big.matrix. See read.big.matrix and the package bigmemory for more details.

Value

A big.matrix object corresponding to a file-backed big.matrix. It's ready to be used as the design matrix X in biglasso and cv.biglasso.

Author(s)

Yaohui Zeng and Patrick Breheny

Maintainer: Yaohui Zeng <yaohui.zeng@gmail.com>

Examples

## see the example in "biglasso-package"

biglasso

Extending Lasso Model Fitting to Big Data

v1.4.1

GPL-3

Authors

Yaohui Zeng [aut,cre], Chuyi Wang [aut,cre], Patrick Breheny [ctb]

Initial release

2021-01-29