Please help with cnv-seq output

[younko]

I read several posting related with cnv-seq output.. but still have some questions. (http://seqanswers.com/forums/showthread.php?t=16882)

When I got the result from cnv-seq, I have th following result. As you can see I have several lines which have significant pvalue but no cnv number or no cnv.pvalue. and in the same way, several lines wiich have significant pvalue with cnv number and cnv.pvalue. what is those difference?

Pvalue itself is not trustful? Do I just have to see the cnv.pvalue??

Please help with this!

"chr5" 180663341 180701730 6 18 180682536 -1.58349117526084 9.82299240634492e-17 0 NA NA NA
"chr5" 180682536 180720925 11 43 180701730 -1.96536181060448 3.39684019358135e-21 0 NA NA NA
"chr5" 180701731 180740120 47 62 180720926 -0.398136133248921 0.00620936069953809 0 NA NA NA
"chr5" 180720926 180759315 713 591 180740120 0.272215271726673 0.0423800701757286 0 NA NA NA
"chr5" 180740121 180778510 712 597 180759316 0.255617635161909 0.0526152496438912 0 NA NA NA
"chr5" 180759316 180797705 53 83 180778510 -0.645647651323409 3.81296507663028e-05 4144 115171 -0.991771308364374 1.70335694939537e-45
"chr5" 180778511 180816900 37 81 180797706 -1.12892531179536 6.69646184005223e-11 4144 115171 -0.991771308364374 1.70335694939537e-45
"chr5" 180797706 180836095 38 69 180816900 -0.859125617874267 1.58258808831096e-07 4144 115171 -0.991771308364374 1.70335694939537e-45
"chr5" 180816901 180855290 33 52 180836096 -0.654574273322322 3.0846549913038e-05 4144 115171 -0.991771308364374 1.70335694939537e-45
"chr5" 180836096 180874485 23 70 180855290 -1.60424973542764 5.43648246376174e-17 4144 115171 -0.991771308364374 1.70335694939537e-45
"chr5" 180855291 180893680 30 71 180874486 -1.24138519843585 2.33599758743762e-12 4144 115171 -0.991771308364374 1.70335694939537e-45
"chr5" 180874486 180912875 33 35 180893680 -0.0834175721261962 0.297461789422106 0 NA NA NA
"chr5" 180893681 180932070 12 12 180912876 0.00147132546031685 0.49625594430728 0 NA NA NA

[arcolombo698]

hi.

First, it is hard to see from your post but here is some sample data.

head(complete_cases)
chromosome start end test ref position log2 p.value cnv
7037 chr7 8766857 8769349 321 633 8768103 -0.6004089 2.820446e-05 31
7038 chr7 8768103 8770595 285 593 8769349 -0.6778468 3.514478e-06 31
7039 chr7 8769349 8771841 248 496 8770595 -0.6207767 1.653367e-05 31
7040 chr7 8770595 8773087 251 516 8771841 -0.6604604 5.677115e-06 31
7681 chr7 9569281 9571773 348 697 9570527 -0.6228480 1.565073e-05 32
7682 chr7 9570527 9573019 393 781 9571773 -0.6115699 2.107484e-05 32
cnv.size cnv.log2 cnv.p.value
7037 4985 -0.6389403 1.572211e-17
7038 4985 -0.6389403 1.572211e-17
7039 4985 -0.6389403 1.572211e-17
7040 4985 -0.6389403 1.572211e-17
7681 4985 -0.6303064 3.839150e-17
7682 4985 -0.6303064 3.839150e-17



The CNV is an index for the window which have different sizes.
So 7037-7040 are all the same window index. Now notice that the log2, for each row is slightly different. but the log2.cnv are all the same for the same cnv window index. Same with cnv.pvalue, this are just grouped together by window index.

Now, the puzzling question as to why data is missing, and some data has complete entries and other data does not, I would suggest to make your parameters much more strict, and then filter out the missing data.

[xiechao]

Each row describes one sliding window position, so the columns "p.value" and "log2" are for that window. Then there is a column called "cnv", which is saying whether that window is part of a CNV region (0 means no, value of 1 or more refers to the CNVR id). If the window is not part of a CNV Region (ie column "cnv" is 0), then the "cnv.*" columns will show value "NA", because they refers to the whole CNV Region.
If the window is part of a CNVR, then cnv.size, cnv.log2, cnv.p.value are used to describe this CNVR (cnv.log2 is calculated from the whole CNV Region covering multiple windows).