sigaR (version 1.18.0)

cghSeg2order: Genomic ordering of cghSeg-objects.

Description

Orders the features within a cghSeg-object in accordance with their genomic order.

Usage

cghSeg2order(CNdata, chr, bpstart, verbose=TRUE)

Arguments

CNdata

Object of class cghSeg.

chr

Column in the slot featureData of the cghSeg-object specifying the chromosome information of the features.

bpstart

Column in the slot featureData of the cghSeg-object specifying the start basepair information of the features.

verbose

Logical indicator: should intermediate output be printed on the screen?

Value

Object of class cghSeg, now genomically ordered.

References

Van de Wiel, M.A., Kim, K.I., Vosse, S.J., Van Wieringen, W.N., Wilting, S.M. , Ylstra, B. (2007), "CGHcall: an algorithm for calling aberrations for multiple array CGH tumor profiles", Bioinformatics, 23, 892-894.

See Also

cghSeg.

Examples

# load data
data(pollackCN16) 

# transform the cghCall-object to a cghSeg-object
pollackCN16 <- cghCall2cghSeg(pollackCN16)

# order the copy number data genomically
pollackCN16 <- cghSeg2order(pollackCN16, 1, 2)