outputs from bulk sequencing

[pirlowang]

Hi
I am successful in completing CaSpER process for my bulk sequencing data. I can not export detailed as to see median or mean log ratio for each segment. I did segment CNV summrization below:

gamma <- 6
all.segments <- do.call(rbind, lapply(final.objects, function(x) x@segments))
segment.summary <- extractSegmentSummary (final.objects)
loss <- segment.summary$all.summary.loss
gain <- segment.summary$all.summary.gain
loh <- segment.summary$all.summary.loh
loss.final <- loss[loss$count>gamma, ]
gain.final <- gain[gain$count>gamma, ]
loh.final <- loh[loh$count>gamma, ]

Then I head all.segments and got this:
ID chr start end state median event_scale size num.marks arm.size.perc
1_vs_1.1 X12_05527 10p 14061 988341 2 -0.56923077 974280 10 0.02447940
1_vs_1.2 X12_05527 10p 988434 14871741 3 0.01769231 large_scale 13883307 159 0.34882681
1_vs_1.3 X12_05527 10p 14877416 17800868 2 -0.33230769 2923452 38 0.07345357
1_vs_1.4 X12_05527 10p 17809348 30717266 3 0.10000000 focal 12907918 142 0.32431955
1_vs_1.5 X12_05527 10p 30820207 32232245 2 -0.40500000 1412038 18 0.03547834
1_vs_1.6 X12_05527 10p 32266289 38689068 3 0.11000000 focal 6422779 78 0.16137636
MeanDev medianDev nVarSite states2
1_vs_1.1 0.112083333333333 0.1 24 del
1_vs_1.2 0.137336152219873 0.14 473 cnloh
1_vs_1.3 0.126 0.13 40 del
1_vs_1.4 0.157622149837134 0.15 307 cnloh
1_vs_1.5 0.136875 0.14 48 del
1_vs_1.6 0.112054794520548 0.11 73 cnloh

I can't understand meaning of median and nVarSite.

Thanks for your help