big_read: Read a file as FBM

In bigstatsr: Statistical Tools for Filebacked Big Matrices

Read a file as FBM

Description

Read a file as a Filebacked Big Matrix by using package {bigreadr}. For a mini-tutorial, please see this vignette.

Usage

big_read(
  file,
  select,
  filter = NULL,
  type = c("double", "float", "integer", "unsigned short", "unsigned char", "raw"),
  backingfile = drop_ext(file),
  ...
)

Arguments

file	File to read.
select	Indices of columns to read (sorted). The length of select will be the number of columns of the resulting FBM.
filter	Vector used to subset the rows of each data frame.
type	Type of the Filebacked Big Matrix (default is double). Either "double" (double precision – 64 bits) "float" (single precision – 32 bits) "integer" "unsigned short": can store integer values from 0 to 65535. It has vocation to become the basis for a FBM.code65536. "raw" or "unsigned char": can store integer values from 0 to 255. It is the basis for class FBM.code256 in order to access 256 arbitrary different numeric values. It is used in package bigsnpr.
backingfile	Path to the file storing the FBM data on disk. An extension ".bk" will be automatically added. Default uses file without its extension.
...	Arguments passed on to bigreadr::big_fread2 nb_parts Number of parts in which to split reading (and transforming). Parts are referring to blocks of selected columns. Default uses part_size to set a good value. skip Number of lines to skip at the beginning of file. progress Show progress? Default is FALSE. part_size Size of the parts if nb_parts is not supplied. Default is 500 * 1024^2 (500 MB).

Value

A Filebacked Big Matrix of type type with length(select) columns.

bigstatsr documentation built on Sept. 11, 2024, 7:08 p.m.