readIdatFiles: Read BeadScan gene expression output

In markdunning/beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

Description

Function to read IDAT files into beadarray.

Usage

readIdatFiles(idatFiles = NULL)

Arguments

idatFiles

A vector of file paths to the idat files that are to be read.

Details

This function allows IDAT files, produced during the BeadArray scanning, to be read directly into beadarray. This removes the requirement to use Illumina's GenomeStudio software to convert such files into an ASCII format before they can be processed.

The expection is that IDAT files from expression BeadArrays will be read using this function. However, this is not currently checked for explicitly and it is possible that files from other platforms may be read successfully.

If files from a two-colour array are to be read, they should all be listed in the idatFiles argument. The function will determine two-colour data is present and act accordingly. If unequal numbers of green and red files are supplied, or the names of the array sections do not match, the function will fail.

IDAT files often contain probes that are used as internal controls and are not annotated by Illumina. Such probes are not included in the output of this function.

Value

An ExpressionSetIllumina object.

Author(s)

Mike Smith

markdunning/beadarray documentation built on May 9, 2019, 8:35 a.m.