fe.read {aCGH.Spline}R Documentation

Function to read Feature Extraction files.

Description

Recommended feature extraction file reading function.

Usage

fe.read(file, Raw=TRUE)

Arguments

file - the feature extraction file to read.
Raw - the intensity values to extract (TRUE = background subtracted values, FALSE = Agilent normalised values).

Details

This function is capable of reading a FE file containing 1 million rows of data within 2 minutes.

Its also flags data points based on Feature extraction exculsion criteria and low intensity probes (cy5 + cy3 < 100).

Value

A dataframe containing eight columns (".temp" format):

- Log2 ratio values.
- Cy5 intensity values.
- Cy3 intensity values.
- Chromosome number.
- Start position.
- Stop position.
- An index.
- A flag.

Note

If the flag is equal to 1 the probe should be removed from further analysis.

The index can be used as a unique indentifier, it is the extact row where the data was taken from the FE file.

The function draws on methods contained within the "Jspline" class for increased speed performance.

Author(s)

Tomas William Fitzgerald

Examples

# data <- FeRead("FEfile.txt")

[Package aCGH.Spline version 2.2 Index]