beadarraySNP (version 1.38.0)

copynumberConversion: Conversion to Copynumber analysis objects

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

Value

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

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.

See Also

SnpSetIllumina-class, aCGH-class, SegList-class