FASeg: An R package that performs forward-backward fragment assembling segmentation for array-CGH and SNP array data

Tianwei Yu, Wei Sun & Ker-Chau Li

The current version is 2.0.

Some bugs in handling 500K SNP arrays are fixed. Segment-wise CNV analysis is added to the gene.cn() function.

download windows version

download mac version (source package)

Another subroutine for compressing the per-probe copy numbers to segment-wise copy numbers

Sample code

The purpose of this package is to provide segmentation utility for array-based copy number data, within the R platform. The core function is "faseg()". It accepts a simple data frame/matrix input, thus can be easily adapted for other data. The input looks like this (the row names are unimportant):

Because there are multiple versions of Affy SNP arrays and platforms from other vendors that can be used for copy number analysis, we stopped developing platform-specific subroutines after the 500K SNP arrays.

Several supporting utilities are also included. They provide data processing for SNP array data, and visualization of the copy numbers. Array-CGH data can be easily used without any pre-processing. The general workflow is shown below, where blue texts represent functions in the package.

read.CNAT.plain()

read.CNT()

SNP.to.cn()

 

faseg()

 

gene.cn()

 

cgh.image()

present.batch()

present.change()

present.two.enzyme()