nim.read {aCGH.Spline}R Documentation

Function to read a Nimblegen "SEG_MNT.txt" file.

Description

Function to read a Nimblgen "SEG_MNT.txt" file.

Usage

nim.read(file, Raw)

Arguments

file - Nimblegen "SEG_MNT.txt" file to read.
Raw - to use raw data or not (TRUE or FALSE).

Details

This function reads the contains of a Nimblegen "SEG_MNT.txt" file into a ".temp" formatted dataframe and flags low intensity probes.

Value

The ".temp" dataframe contains eight columns:

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

Note

This function reads spatially normalised intensity values from the Nimblegen input file.
There is currently no option to output a "SEG_MNT.txt" format, however, signal-map gff format is supported.

Author(s)

Tomas William Fitzgerald

See Also

http://www.nimblegen.com/

Examples

# data <- nim.read("Nimblegen_SEG_MNT.txt")

[Package aCGH.Spline version 2.2 Index]