[ < ] [ > ]   [ << ] [ Up ] [ >> ]         [Top] [Contents] [Index]

6.3 Sample ibddrop output

Run the first example with the command:

 
ibddrop parIBD_LL

The genetic map is given, semi-graphically, in the following manner,

 
 Distances (cM):

              T1                       
 --------------+---------------------  
   44.6   22.3   22.3   11.2   11.2    
 +------+-------------+------+------+  
M1     M2            M3     M4     M5  

Check the parameter file to verify that this is indeed what we wanted. Since we had two `set proband gametes' statements, we have two sets of results. Let's take a closer look at the second one,

 
Summary for component 2:

   Probabilities of IBD patterns  (pedigree based)

      Proband gamete set 1:  5v1 0  5v1 1  3v1 0  3v3 1

      pattern marker-1 marker-2  trait-1 marker-3 marker-4 marker-5    label

      1 1 1 1    .0315    .0306    .0314    .0300    .0273    .0284        0
      1 1 1 2    .0295    .0294    .0284    .0295    .0317    .0307        1
      1 1 2 1    .0131    .0126    .0149    .0127    .0129    .0123        3
      1 1 2 2    .0097    .0106    .0100    .0097    .0089    .0092        4
      1 1 2 3    .0255    .0286    .0263    .0276    .0279    .0283        5
      1 2 1 1    .0638    .0635    .0658    .0644    .0645    .0650        6
      1 2 1 2    .0056    .0059    .0056    .0056    .0069    .0066        7
      1 2 1 3    .0581    .0595    .0589    .0609    .0593    .0590        8
      1 2 2 1    .0683    .0720    .0648    .0683    .0703    .0682        9
      1 2 2 2    .0520    .0488    .0494    .0490    .0491    .0487       10
      1 2 2 3    .1370    .1351    .1366    .1359    .1349    .1355       11
      1 2 3 1    .1369    .1303    .1366    .1316    .1348    .1379       12
      1 2 3 2    .0275    .0265    .0296    .0265    .0266    .0269       13
      1 2 3 3    .0965    .1013    .0961    .0997    .0974    .1009       14
      1 2 3 4    .2449    .2454    .2455    .2488    .2473    .2425       15

The probabilities are summarized by ibd "pattern". A pattern is a series of integers with the same length as the number of gametes to score. Same numbers indicate gametes that are ibd. For instance, `1 1 1 1' means all four gametes are ibd; `1 2 1 1' means gametes 1, 3, and 4 are ibd, while gamete 2 is not ibd with the others; `1 2 3 4' means all four gametes are not ibd.

The ibd patterns are scored for each locus separately; there is a column for each of the five markers and one for the trait.

The second example can be run as:

 
ibddrop parIBD_WU

And the interesting part of the output is

 
Summary for component 2:

   Probabilities of ibd patterns

      Proband gamete set 1:  5v1 0  5v1 1

        ibd  wndw 1 wndw 2 wndw 3 wndw 4

      0 0 0   .7231  .7447  .7659  .7874
      0 0 1   .0668  .0686  .0464  .0475
      0 1 0   .0670  .0519  .0360  .0266
      0 1 1   .0321  .0230  .0409  .0265
      1 0 0   .0901  .0675  .0691  .0472
      1 0 1   .0081  .0083  .0067  .0050
      1 1 0   .0088  .0239  .0162  .0281
      1 1 1   .0040  .0121  .0190  .0318

The ibd pattern is given as a series of zeros and ones with the same length as the number of loci in the window (the window size). `1' means that all gametes are ibd at that locus and `0' means, well, take a wild guess!


[ < ] [ > ]   [ << ] [ Up ] [ >> ]         [Top] [Contents] [Index]

This document was generated using texi2html