jointseg (version 1.0.2)

doPSCN: Run PSCN segmentation (defunct)

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

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

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

# }