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Last data update: 2014.03.03

R: Mean Segmentation

segmented_signal

R Documentation

Mean Segmentation

Description

Multiple profile mean segmentation on the genomic signal is performed using the multiseg function of the cghseg package. Heterogeneous genomic profiles can only be analysed if allocated to homogeneous groups.

Usage

segmented_signal(SNP.Chr, group)

Arguments

`SNP.Chr`	SNP/CGH profile matrix for a given chromosome not containing NA's. Columns correspond to patients and rows to probes.
`group`	Indicator denoting the different variance groups among the patients. By default, all genomic profiles allocated to one group.

Value

Smoothed genomic signal matrix. Rows correspond to probes and columns to patients.

Author(s)

E. I. Delatola, E. Lebarbier, T. Mary-Huard, F. Radvanyi, S. Robin, J. Wong.

References

Picard, F., Lebarbier, E., Hoebeke, M., Rigaill, G., Thiam, B., Robin, S. (2011). Joint segmentation, calling, and normalization of multiple CGH profiles. Biostatistics.

Examples

#data(SNP)
#mu.SNP = segmented_signal(SNP ,rep(1,dim(SNP)[2]))