mpsmooth {mpss} | R Documentation |
Multi-Platforms segmentation for detection of CNVs
mpsmooth(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), del.lim = -0.05, dup.lim=0.05, min.probes = 10, min.probe.density = 5, min.length = 1000, min.dist = 5000, fdr.limit = 1e-05)
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 platform 3 is unavailable |
pos4 |
Same as pos1 , but for platform 4. Set to NA if platform 4 is unavailable. |
data1 |
Normalized intensity ratio for platform 1, corresponding to each position in pos1 .
A list where each component corresponds to each chromosome. See Details. |
data2 |
Same as data1 , but for platform 3. |
data3 |
Same as data1 , but for platform 4.
Set this to NA if there is no platform 3 available. |
data4 |
Same as data1, but for platform 3. 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. |
del.lim |
Threshold for deletions. See Details. |
dup.lim |
Threshold for duplications. See Details. |
min.probes |
Minimum number of probes in region. |
min.probe.density |
Minimum number of probes per kb in region. |
min.length |
Minimum length of CNV regions (in bases). |
min.dist |
Two regions will be merged if the distance between them is less than min.dist (in bases). |
fdr.limit |
Fdr threshold to define significant segments. See Details. |
This is a convenient wrapper function that performs smoothing using smoothseg2
for all the chromosomes present in the input
and then performs segmentation using segmentation
, and returns regions that pass the user specified thresholds.\
Users are advised to first perform background normalization to minimize any platform-specific effects.
For data from germline DNA, we recommend that users apply srsmooth
to the unnormalized data in
a chromosome-by-chromosome fashion, and use the 'residual' as input to this function.\
Deletions are sets of consecutive probes for which the smoothed intensities ars consistently smaller than or equal to del.lim
.
Duplications are sets of consecutive probes for which the smoothed intensities ars consistently greater than or equal to dup.lim
.
False Discovery rates are calculated from the p-values using Benjamini and Yekutieli's method. See p.adjust
.
cnv |
A data frame with the following columns:
start : Start position of CNV regions.
end : End position of CNV regions.
chr : Chromosome number of CNV regions.
start.loc : Index of start position in unlist(pos) .
end.loc : Index of end position in unlist(pos) .
length : length of region.
p : p-value.
fdr : false discovery rate.
numprobes : number of probes in the region.
scaled_x2 : scaled chi squared value.
cn : copy number status, 1 for deletion and 3 for duplication.
m : mean of the probe intensities in the region.
sd : standard deviation of the probe intensities in the region.
pt : p value for test of discrepant regions.
t_fdr : FDR for test of discrepant regions.
m1 : mean of the probe intensities from platform 1 in the region.
m2 : same as m1 but for platform 2.
m3 : same as m1 but for platform 3.
m4 : same as m1 but for platform 4.
sd1 : standard deviation of the probe intensities from platform 1 in the region.
sd2 : same as sd1 but for platform 2.
sd3 : same as sd1 but for platform 3.
sd4 : same as sd1 but for platform 4.
|
y |
Smooth segmented values corresponding to each position in pos . |
pos |
Union of the probe positions in the platforms 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 s = mpsmooth(pos1 = affyx, pos2 = illumx, pos3 = NA, pos4 = NA, data1 = affy, data2 = illum, data3 = NA, data4 = NA, maxiter = 50, lambda = 100, lambda.range = c(20,600) , del.lim = -0.05, dup.lim=0.05, min.probes = 10, min.probe.density = 5, min.length = 1000, min.dist = 5000, fdr.limit = 1e-05)