doPSCN: Run PSCN segmentation (defunct)

In mpierrejean/jointSeg: Joint Segmentation of Multivariate (Copy Number) Signals

Description

The 'PSCN' package is not maintained anymore and it is not available for R >= 3.0.0. The original 'doPSCN' function has been moved to the directory 'zzz.defunct'. The skeleton of that function is kept for backward compatibility.

Usage

doPSCN(Y, alpha = 0.01, platform = c("Illumina", "Affymetrix"),
  verbose = FALSE, ...)

Arguments

Y	The signal to be segmented, a matrix containing the following columns: c Total copy number (log scale) b Allele B fraction (a.k.a. BAF)
alpha	sensitivity level in [0,1] to be passed to PSCN::segmentation.
platform	Specifies form which array platform 'Y' was generated: Illumina or Affymetrix
verbose	A logical value: should extra information be output ? Defaults to FALSE.
...	Further arguments to be passed to PSCN::smoothing

Author(s)

Morgane Pierre-Jean and Pierre Neuvial

References

Chen, H., Xing, H., & Zhang, N. R. (2011). Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays. PLoS computational biology, 7(1), e1001060.

See Also

PSSeg

Examples

print("The 'PSCN' package is not available for R >= 3.0.0.")
print("See http://cran.r-project.org/web/packages/PSCN/index.html")

mpierrejean/jointSeg documentation built on May 23, 2019, 6:28 a.m.