mpsmoothseg {mpss} | R Documentation |
Performs segmentation on intensity data from various platforms for a single chromosome.
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))
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. |
Currently, the function allows a maximum of 4 platforms.
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. |
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))