PSEUDO -- Linkage Peak Summaries
When you run PSEUDO, you may be interested in saving some of the results from the simulated genome scans. Although it's not practical to
save (or even print) all the simulated lod scores for every position, it can be useful to save maximum genomewide or chromosome wide lod values
Printing maximum lod scores for each simulated genome
To tell PSEUDO to save the genomewide lod score, use the --simpeaks option. If you try this out for the simulated data we've looked at,
PSEUDO will create a file called pseudo.simmax that probably looks something like this:
MAXIMUM LOD SCORE BY SIMULATED GENOME FOR Hypothesis_0 AND Hypothesis_1
[SIMULATIONS 1 to 100000]
SIMULATION MAXIMUM LOD
==============================
1 1.32600
2 1.72513
3 1.81475
4 1.84240
5 1.86913
6 2.01796
7 1.64834
8 1.71604
9 1.52708
10 1.72909
11 1.03668
12 0.98130
13 0.84666
14 1.17512
15 1.12696
16 1.62577
17 1.04175
18 1.43534
19 2.99845
20 1.39591
You may notice that this table reports values for both Hypothesis_0 and Hypothesis_1. If you look at the hypothesis
file, you'll see that
Hypothesis_0 and Hypothesis_1 test different lod values and ranks, but share the same outcome
affection [ALL], affection [PAIRS]
PSEUDO attempts to make output file sizes as reasonable as possible, and will print only one table of values for each
unique outcome.
Maximum lod scores by chromosome
You can also tell PSEUDO to print out the maximum lod score for each chromosome (using the --peaks option). For our example data set, you'll get a table similar to
MAXIMUM LOD SCORE PER CHROMOSOME BY SIMULATED GENOME FOR Hypothesis_0 AND Hypothesis_1
[SIMULATIONS 1 to 50000]
SIMULATION CHROMOSOME MAXIMUM LOD
====================================
1 1 0.01460
1 2 -0.00494
1 3 0.22683
1 4 0.22949
1 5 1.94824
1 6 0.03867
1 7 0.81997
1 8 0.10371
1 9 0.29101
1 10 0.26386
1 11 0.41618
1 12 0.10728
1 13 0.61914
1 14 0.32498
1 15 0.36957
1 16 0.69132
1 17 0.00344
.
.
.
Distribution of hits for compound outcomes
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