joint.segmentation: Joint Segmentation on log2ratio and log2mBAF Dimensions
In saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Description Usage Arguments Value Author(s) References See Also Examples

We employ the algorithm developed by (Zhang et al., 2010) to perform joint segmentation on log2ratio and log2mBAF dimensions. The function outputs the starting and ending points of each CNV segment as well as some summary statistics.

1 2	joint.segmentation(data, min.snps = 10, global.pval.cutoff = 1e-04, max.chpts = 30, verbose = TRUE)

`data`	a data frame containing log2ratio and log2mBAF data generated by `cnv.data`.
`min.snps`	the minimum number of probes a segment needs to span.
`global.pval.cutoff`	the p-value cut-off a (or a pair) of change points to be determined as significant in each cycle of joint segmentation.
`max.chpts`	the maximum number of change points to be detected for each chromosome.
`verbose`	logical. If more details to be output. Default is `TRUE`.

A data frame containing the starting and ending points of each CNV segment as well as some summary statistics.

Zhongyang Zhang <zhongyang.zhang@mssm.edu>

Zhang, N. R., Siegmund, D. O., Ji, H., Li, J. Z. (2010) Detecting simultaneous changepoints in multiple sequences. Biometrika, 97:631–645.

cnv.data

data(seq.data)

## Not run: 
seq.segs <- joint.segmentation(data=seq.data, min.snps=10, 
                               global.pval.cutoff=1e-4, max.chpts=30, 
                               verbose=TRUE)

## End(Not run)

## how the joint segmentation results look like
data(seq.segs)
head(seq.segs)

Loading required package: RANN
Loading required package: DNAcopy
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  19.07324 
Split 1: 1352, Z-score = 1931.333.
Split 2: 1408, 2100, Z-score = 575.4419.
Split 3: 496, Z-score = 300.6507.
Split 4: 228, 281, Z-score = 154.8601.
Split 5: 927, 1193, Z-score = 30.25359.
Maximum Z-score is 18.90765, which does not exceed cutoff of 19.07324. Segmentation finished.
finish segmentation of chr = 1 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.68457 
Split 1: 1132, 1699, Z-score = 31.39634.
Maximum Z-score is 17.89262, which does not exceed cutoff of 18.68457. Segmentation finished.
finish segmentation of chr = 2 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.49023 
Split 1: 1691, Z-score = 21.2497.
Maximum Z-score is 15.59223, which does not exceed cutoff of 18.49023. Segmentation finished.
finish segmentation of chr = 3 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.71289 
Split 1: 338, Z-score = 445.8931.
Split 2: 91, 104, Z-score = 35.01532.
Maximum Z-score is 8.183044, which does not exceed cutoff of 17.71289. Segmentation finished.
finish segmentation of chr = 4 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.10156 
Split 1: 332, Z-score = 251.8271.
Split 2: 754, Z-score = 31.17119.
Split 3: 79, Z-score = 24.00421.
Maximum Z-score is 14.10851, which does not exceed cutoff of 18.10156. Segmentation finished.
finish segmentation of chr = 5 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.2959 
Split 1: 625, 1154, Z-score = 19.51223.
Maximum Z-score is 13.13717, which does not exceed cutoff of 18.2959. Segmentation finished.
finish segmentation of chr = 6 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.2959 
Split 1: 841, Z-score = 178.5739.
Split 2: 137, Z-score = 23.28715.
Split 3: 497, 772, Z-score = 18.45078.
Maximum Z-score is 12.54297, which does not exceed cutoff of 18.2959. Segmentation finished.
finish segmentation of chr = 7 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.71289 
Split 1: 387, Z-score = 2762.917.
Split 2: 425, Z-score = 115.5748.
Split 3: 887, Z-score = 53.92861.
Split 4: 465, 498, Z-score = 18.48459.
Maximum Z-score is 14.52751, which does not exceed cutoff of 17.71289. Segmentation finished.
finish segmentation of chr = 8 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.90723 
Split 1: 875, Z-score = 23.29696.
Maximum Z-score is 11.11354, which does not exceed cutoff of 17.90723. Segmentation finished.
finish segmentation of chr = 9 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.71289 
Split 1: 272, 331, Z-score = 224.9744.
Split 2: 232, 243, Z-score = 93.58962.
Split 3: 372, 391, Z-score = 85.4413.
Maximum Z-score is 12.61328, which does not exceed cutoff of 17.71289. Segmentation finished.
finish segmentation of chr = 10 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.2959 
Split 1: 12, 119, Z-score = 30.43728.
Split 2: 907, 1009, Z-score = 34.07183.
Split 3: 1660, Z-score = 32.58678.
Split 4: 1175, 1606, Z-score = 18.37915.
Maximum Z-score is 12.80469, which does not exceed cutoff of 18.2959. Segmentation finished.
finish segmentation of chr = 11 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.2959 
Split 1: 121, 1208, Z-score = 30.95737.
Split 2: 550, 898, Z-score = 25.90753.
Maximum Z-score is 13.98394, which does not exceed cutoff of 18.2959. Segmentation finished.
finish segmentation of chr = 12 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  16.74121 
Split 1: 275, Z-score = 788.0796.
Maximum Z-score is 15.69866, which does not exceed cutoff of 16.74121. Segmentation finished.
finish segmentation of chr = 13 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.71289 
Split 1: 920, Z-score = 35.13348.
Maximum Z-score is 17.27245, which does not exceed cutoff of 17.71289. Segmentation finished.
finish segmentation of chr = 14 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.71289 
Split 1: 324, 568, Z-score = 23.5499.
Maximum Z-score is 15.76477, which does not exceed cutoff of 17.71289. Segmentation finished.
finish segmentation of chr = 15 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.71289 
Split 1: 524, Z-score = 1270.419.
Split 2: 942, Z-score = 28.27943.
Maximum Z-score is 14.53416, which does not exceed cutoff of 17.71289. Segmentation finished.
finish segmentation of chr = 16 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.2959 
Split 1: 354, Z-score = 1854.383.
Maximum Z-score is 15.83231, which does not exceed cutoff of 18.2959. Segmentation finished.
finish segmentation of chr = 17 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  16.74121 
Maximum Z-score is 10.56861, which does not exceed cutoff of 16.74121. Segmentation finished.
finish segmentation of chr = 18 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  18.68457 
Split 1: 962, 1051, Z-score = 19.85533.
Maximum Z-score is 9.065886, which does not exceed cutoff of 18.68457. Segmentation finished.
finish segmentation of chr = 19 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.32422 
Split 1: 218, Z-score = 613.9186.
Split 2: 147, 194, Z-score = 186.8088.
Split 3: 71, 81, Z-score = 19.6974.
Maximum Z-score is 16.92412, which does not exceed cutoff of 17.32422. Segmentation finished.
finish segmentation of chr = 20 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  16.74121 
Split 1: 23, Z-score = 33.40338.
Split 2: 320, Z-score = 25.51607.
Maximum Z-score is 12.70774, which does not exceed cutoff of 16.74121. Segmentation finished.
finish segmentation of chr = 21 
Computing threshold for weighted chi-square...
MSCBS: weighted chisquare cutoff =  17.32422 
Maximum Z-score is 9.227731, which does not exceed cutoff of 17.32422. Segmentation finished.
finish segmentation of chr = 22 
   chr  posStart    posEnd   length chrIdxStart chrIdxEnd numProbe
1 chr1    801943  16731510 15929568           1       228      228
2 chr1  16890428  17275054   384627         229       281       53
3 chr1  17297289  31426815 14129527         282       496      215
4 chr1  31732602  60503594 28770993         497       927      431
5 chr1  60505783 107870899 47365117         928      1193      266
6 chr1 108113856 120455441 12341586        1194      1352      159
  log2ratio.Mean log2ratio.SD log2ratio.Median log2ratio.MAD log2mBAF.Mean
1     -0.5624744    0.4986741       -0.5949604     0.5336560    0.56069308
2     -0.2978404    0.5491663       -0.2897923     0.4047772   -0.02760742
3     -0.5175220    0.5376744       -0.5184167     0.5337303    0.56839298
4     -0.1095851    0.4770595       -0.0880312     0.4519774    0.16125862
5     -0.4161586    0.5397789       -0.4463434     0.4396174    0.16197340
6     -0.1754930    0.4602296       -0.1518777     0.3573186    0.17596483
  log2mBAF.SD log2mBAF.Median log2mBAF.MAD
1   0.2220726      0.58496250    0.1908776
2   0.2565385     -0.06509503    0.2258865
3   0.2423265      0.60145062    0.2264163
4   0.2409466      0.16551790    0.2318938
5   0.2532963      0.16294034    0.2633028
6   0.2591824      0.17508671    0.2806928