CopynumberConversion: Conversion to Copynumber analysis objects

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

SnpSetIllumina objects are converted to other objects for numerical analysis

Usage

  convert2aCGH(object,normalizedTo=2,doLog=TRUE,organism="hsa")
  convert2SegList(object,normalizedTo=2,doLog=TRUE,organism="hsa")

Arguments

object	SnpSetIllumina object
normalizedTo	numeric, 'normal' copynumber datavalue for object
doLog	logical, perform logarithmic transformation (log2)
organism	character, organism used in object. Currently 'hsa' and 'mmu' are recognized. Used to convert sex chromosomes to their proper numerical representation

Details

These functions produce objects that can be used by the analysis functions in the aCGH or snapCGH packages. The SnpSetIllumina intensity values are stored in a linear scale. Both types of objects assume a logarithmic scale, so by default the values are transformed to a log2 scale centered around 0.

Value

convert2aCGH returns a aCGH object as used in the aCGH package. convert2SegList returns a SegList object as used in the snapCGH package.

Author(s)

Jan Oosting

See Also

SnpSetIllumina-class, aCGH-class, SegList-class

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.