mpsmoothseg {mpss}R Documentation

Multi-Platforms Segmentation for Detection of Copy Number Variations

Description

Performs segmentation on intensity data from various platforms for a single chromosome.

Usage

smoothseg2(pos1 = pos1 ,pos2 = pos2, pos3 = NA, pos4 = NA, data1 = data1, data2 = data2, data3 = NA,
data4 = NA, maxiter= 20, lambda = NA, lambda.range = c(20,600))

Arguments

pos1 Probe positions for platform 1. A list where each component corresponds to each chromosome. See Details.
pos2 Same as pos1, but for platform 2.
pos3 Same as pos1, but for platform 3. Set to NA if there is no platform 3 available
pos4 Same as pos1, but for platform 4. Set to NA if there is no platform 4 available.
data1 Normalized intensity ratio for platform 1, corresponding to each position in pos1. A list where each component corresponds to each chromosome.
data2 Same as data1, but for platform 2.
data3 Same as data1, but for platform 3. Set this to NA if there is no platform 3 available.
data4 Same as data1, but for platform 4. Set this to NA if there is no platform 4 available.
maxiter Maximum number of iterations in the iterative backfitting algorithm.
lambda A user defined value that determines the degree of smoothness, high value of lambda means we impose a smoother estimate. Set this to NA if one wishes to use AIC criteria to choose the optimal lambda
lambda.range The range of lambda to search for optimal lambda using AIC criteria.

Details

Currently, the function allows a maximum of 4 platforms.

Value

pos Union of the probe positions in the platforms used.
y Smooth segmented values corresponding to each position in x.
sig2 Mean of the estimated platform specific error variances.
wy Diagonal entries for Z'WZ.
aic AIC value.
df Degrees of Freedom associated with the random effect parameter.
logp Sum of log densities of $y_ij|f$.
lambda lambda value used.
chi probe specific contribution to chi-squared statistic.

See Also

mpsmooth,segmentation

Examples

setwd(paste(searchpaths()[grep("mpss",searchpaths())],'/data/',sep=""))
load("illum12056.Rdata") #Illumina platform
#norm_y contains the normalized intensity ratios for chromosome 1 and 2.
#norm_x contains the corresponding probe locations.
illum = norm_y
illumx = norm_x
load("affy12056.Rdata") #Affymetrix platform
affy = norm_y
affyx = norm_x

#try for Chromosome 1
chr = 1

ss = smoothseg2(pos1 = affyx[[chr]] ,pos2 = illumx[[chr]], pos3 = NA, pos4 = NA, data1 = affy[[chr]], 
data2 = illum[[chr]], data3 = NA, data4 = NA, maxiter = 20, lambda = 100, lambda.range = c(20,600))

[Package mpss version 1.2 Index]