Dear group,

I'm trying to detect copy number variations with the cn.MOPS package. I 
have eight different samples (coming from different individuals 
re-sequenced by Solexa). Sequences have been mapped against the 
reference genome with  BWA, the genome coverage of my samples ranges 
from 13x to 6x. I have run the cn.mops using the package default parameters.
However, when I run the algorithm it detects some CNV regions for which 
the copy number is 2 for all the individuals. Does anyone have an 
explanation for this result?
I paste you here the code I have used and one example of a detected CNV 
where the copy number is 2.

Thanks in advance

Laura

 > sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rsamtools_1.8.6      Biostrings_2.24.1    cn.mops_1.2.6
[4] GenomicRanges_1.8.12 IRanges_1.14.4       Biobase_2.16.0
[7] BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1 stats4_2.15.1  zlibbioc_1.2.0

 > Countsreads_SL2.40ch02<-getReadCountsFromBAM(BAMFiles, 
c("Cervil","Criollo_new","Ferum_new","LA0147","LA1420","Levovil","Plovdiv","Stupike"),refSeqName=c("SL2.40ch02"),mode="unpaired")

 > resCNMOPS_SL2.40ch02<-cn.mops(Countsreads_SL2.40ch02)

 > head(params(resCNMOPS_SL2.40ch02),n=11L)
$method
[1] "cn.mops"
$folds
[1] 0.025 0.500 1.000 1.500 2.000 2.500 3.000 3.500 4.000
$classes
[1] "CN0" "CN1" "CN2" "CN3" "CN4" "CN5" "CN6" "CN7" "CN8"
$priorimpact
[1] 1
$cyc
[1] 20
$normType
[1] "poisson"
$normQu
[1] 0.25
$upperThreshold
[1] 0.5
$lowerThreshold
[1] -0.9
$minWidth
[1] 3
$SegmentationParams
character(0)

 > *Countsreads*_SL2.40ch02[1512]
GRanges with 1 range and 8 elementMetadata cols:
         seqnames               ranges strand |   Levovil Criollo_new 
Ferum_new Stupike   Plovdiv    LA1420    Cervil    LA0147
<Rle> <IRanges> <Rle> | <integer> <integer> <integer> <integer> 
<integer> <integer> <integer> <integer>
   [1] SL2.40ch02 [*43819001, 43848000*]      * | *112         403       
164 **1306      1192      1181       907       617*

     seqlengths:
    SL2.40ch02
            NA

 > *cnvs*(resCNMOPS_SL2.40ch02)[6]
GRanges with 1 range and 4 elementMetadata cols:
         seqnames               ranges strand |  sampleName    
median      mean *CN*
<Rle> <IRanges> <Rle> | <factor> <numeric> <numeric> *<character>*
   [1] SL2.40ch02 [*43819001, 43906000*]      * | Criollo_new 
0.5849618   0.63563 *CN2*

   seqlengths:
    SL2.40ch02
            NA

 > *cnvr*(resCNMOPS_SL2.40ch02)[7]
GRanges with 1 range and 8 elementMetadata cols:
         seqnames               ranges strand | CN.Levovil 
CN.Criollo_new    CN.Ferum_new CN.Stupike CN.Plovdiv CN.LA1420 CN.Cervil 
CN.LA0147
<Rle> <IRanges> <Rle> | <factor> <factor> <factor> <factor> <factor> 
<factor> <factor> <factor>
   [1] SL2.40ch02 [*43819001, 43906000*]      * | *CN2            CN2    
CN2        CN2        CN2       CN2       CN2       CN2*

   seqlengths:
    SL2.40ch02
            NA



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