readClfEnv: Parsing a CLF file using Affymetrix Fusion SDK

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Parsing a CLF file using Affymetrix Fusion SDK

Description

This function parses a CLF file using the Affymetrix Fusion SDK. CLF (chip layout) files contain information associating probe ids with chip x- and y- coordinates.

Usage

readClfEnv(file, readBody = TRUE)

Arguments

file	character(1) providing a path to the CLF file to be input.
readBody	logical(1) indicating whether the entire file should be parsed (TRUE) or only the file header information describing the chips to which the file is relevant.

Value

An environment. The header element is always present; the remainder are present when readBody=TRUE.

header	A list with information about the CLF file. The list contains elements described in the CLF file format document referenced below.
dims	A length-two integer vector of chip x- and y-coordinates.
id	An integer vector of length prod(dims) containing probe identifiers.
x	An integer vector of length prod(dims) containing x-coordinates corresponding to the entries in id.
y	An integer vector of length prod(dims) containing y-coordinates corresponding to the entries in id.

Author(s)

Martin Morgan

See Also

https://www.affymetrix.com/support/developer/fusion/File_Format_CLF_aptv161.pdf describes CLF file content.

HenrikBengtsson/affxparser documentation built on Jan. 7, 2025, 11:46 a.m.