readCelIntensities: Reads the intensities contained in several Affymetrix CEL...

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Reads the intensities contained in several Affymetrix CEL files

Description

Reads the intensities of several Affymetrix CEL files (as opposed to readCel() which only reads a single file).

Usage

 readCelIntensities(filenames, indices = NULL, ..., verbose = 0)

Arguments

filenames	the names of the CEL files as a character vector.
indices	a vector of which indices should be read. If the argument is NULL all features will be returned.
...	Additional arguments passed to readCel().
verbose	an integer: how verbose do we want to be, higher means more verbose.

Details

The function will initially allocate a matrix with the same memory footprint as the final object.

Value

A matrix with a number of rows equal to the length of the indices argument (or the number of features on the entire chip), and a number of columns equal to the number of files. The columns are ordered according to the filenames argument.

Note

Currently this function builds on readCel(), and simply calls this function multiple times. If testing yields sufficient reasons for doing so, it may be re-implemented in C++.

Author(s)

James Bullard and Kasper Daniel Hansen

See Also

readCel() for a discussion of a more versatile function, particular with details of the indices argument.

Examples

  # Scan current directory for CEL files
  files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
  if (length(files) >= 2) {
    cel <- readCelIntensities(files[1:2])
    str(cel)
    rm(cel)
  }

  # Clean up
  rm(files)

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.