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 mac version (source package)
Another subroutine for compressing the per-probe copy numbers to segment-wise copy numbers
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.
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