PSEUDO -- Family Variance Weights
Basic summaries
Once the main simulation runs, PSEUDO also produces a number of summaries of family variance
weights . By default, the program will output two tables for each hypothesis you've tested.
The first table will be a listing of maximum and minimum variance weights for each chromosome.
MAXIMUM AND MINIMUM WEIGHTS BY CHROMOSOME
=========================================
Hypothesis : Hypothesis_5
Affections : trait [QTL]
Target Lod : 1.81
Target Rank : 2
CHR MAX WT FAMILY | MIN WT FAMILY | AVERAGE
----------------------------------------------------------------
1 0.04655 148 | 0.04288 113 | 0.04406
2 0.04601 9 | 0.04284 107 | 0.04406
3 0.04536 194 | 0.04282 164 | 0.04402
4 0.04614 91 | 0.04270 28 | 0.04394
5 0.04587 67 | 0.04295 184 | 0.04394
6 0.04562 26 | 0.04282 59 | 0.04399
7 0.04557 65 | 0.04278 94 | 0.04406
8 0.04567 94 | 0.04288 45 | 0.04397
9 0.04637 35 | 0.04291 125 | 0.04403
10 0.04591 79 | 0.04289 195 | 0.04399
11 0.04568 12 | 0.04259 3 | 0.04403
12 0.04676 188 | 0.04262 151 | 0.04407
13 0.04588 125 | 0.04277 41 | 0.04400
14 0.04566 97 | 0.04265 10 | 0.04398
15 0.04606 189 | 0.04284 72 | 0.04406
16 0.04565 53 | 0.04287 102 | 0.04403
17 0.04561 132 | 0.04288 193 | 0.04401
18 0.04565 185 | 0.04276 72 | 0.04399
19 0.04592 95 | 0.04280 103 | 0.04402
20 0.04622 49 | 0.04260 85 | 0.04401
21 0.04587 101 | 0.04264 186 | 0.04405
22 0.04587 161 | 0.04288 38 | 0.04404
The second presents the same information, on a per-family basis.
MAXIMUM AND MINIMUM WEIGHTS BY FAMILY
=====================================
Hypothesis : Hypothesis_0
Affections : affection [PAIRS], affection [ALL]
Target Lod : 3.60
Target Rank : 1
FAMILY | AVERAGE | MAX WT CHR | MIN WT CHR
----------------------------------------------------------------------------
1 | 0.00647 | 0.00669 5 | 0.00635 17
2 | 0.00649 | 0.00664 18 | 0.00639 12
3 | 0.00648 | 0.00663 15 | 0.00641 5
4 | 0.00650 | 0.00669 8 | 0.00639 12
5 | 0.00649 | 0.00658 5 | 0.00638 7
6 | 0.00647 | 0.00660 20 | 0.00636 4
7 | 0.00649 | 0.00663 16 | 0.00639 19
8 | 0.00648 | 0.00656 5 | 0.00638 10
9 | 0.00646 | 0.00652 4 | 0.00637 16
10 | 0.00647 | 0.00660 11 | 0.00637 13
11 | 0.00645 | 0.00653 10 | 0.00638 11
12 | 0.00648 | 0.00660 9 | 0.00639 4
13 | 0.00648 | 0.00661 7 | 0.00640 4
14 | 0.00647 | 0.00664 22 | 0.00638 11
15 | 0.00649 | 0.00659 4 | 0.00641 21
16 | 0.00650 | 0.00662 3 | 0.00638 17
17 | 0.00650 | 0.00663 4 | 0.00636 12
18 | 0.00647 | 0.00661 5 | 0.00635 2
Optional weight summaries
If you'd like, you can also tell PSEUDO to produce output files that provide more information on family variance
weights. If you're interested only in obtaining the weights for each family and chromosome, try the --weights
option. When this option is selected PSEUDO will write the estimated weight for each family and chromosome
to the file pseudo.weights. For the example data, PSEUDO produced the following weights output:
VARIANCE WEIGHTS BY FAMILY AND CHROMOSOME FOR Hypothesis_0
==========================================================
CHROMOSOME FAMILY WEIGHT
---------------------------------
1 1 0.00645
1 2 0.00655
1 3 0.00650
1 4 0.00643
1 5 0.00657
1 6 0.00644
1 7 0.00651
1 8 0.00644
1 9 0.00645
1 10 0.00648
1 11 0.00643
1 12 0.00643
1 13 0.00648
1 14 0.00645
1 15 0.00642
1 16 0.00648
1 17 0.00639
1 18 0.00650
.
.
.
If you're interested in more detailed information, the --reps option will be useful. For this option,
PSEUDO output all proportions used to calculate each family variance weight.
The table below shows a small portion of the output produced for our example simulation using the pseudo_scan.ped data set.
If you recall, we generated a 20 gene-dropping replicates of the original data to be
used for z-score sampling. If
you look at the look at the column under the "SELECTIONS" heading, the number of times
each of the 20 z-score replicates in the pool for family 1 on chromosome 1 was chosen
is listed; here replicate 1 was chosen 4952 times. Of the simulations where replicate
1 was chosen, 30 were positive for Hypothesis_0, with overall success proportion of
0.00606.
REPLICATE SUMMARY RESULTS FOR Hypothesis_0
==========================================
[CHROMOSOME 1 FAMILY 5001]
REPLICATE SELECTIONS POSITIVE PROP POS
----------------------------------------------------
1 4952 30 0.00606
2 5041 25 0.00496
3 4962 37 0.00746
4 5040 26 0.00516
5 4930 30 0.00609
6 5078 35 0.00689
7 5143 39 0.00758
8 5021 36 0.00717
9 4982 33 0.00662
10 5018 34 0.00678
11 5000 27 0.00540
12 5093 28 0.00550
13 4918 20 0.00407
14 4987 39 0.00782
15 5072 27 0.00532
16 4866 35 0.00719
17 4948 35 0.00707
18 4951 35 0.00707
19 4995 28 0.00561
20 5003 30 0.00600
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