Commit 4637465c authored by damien's avatar damien
Browse files

Added F3-outbred example.

parent d7301388
data type A
1 37 0 0
*M_1_1 2
*M_1_2 2
*M_1_3 2
*M_1_4 0
*M_1_5 2
*M_1_6 2
*M_1_7 2
*M_1_8 2
*M_1_9 0
*M_1_10 2
*M_1_11 2
*M_1_12 2
*M_1_13 2
*M_1_14 2
*M_1_15 0
*M_1_16 0
*M_1_17 0
*M_1_18 0
*M_1_19 2
*M_1_20 0
*M_2_1 0
*M_2_2 0
*M_2_3 2
*M_2_4 0
*M_2_5 0
*M_2_6 0
*M_2_7 0
*M_2_8 0
*M_2_9 2
*M_2_10 2
*M_2_11 0
*M_2_12 0
*M_2_13 2
*M_2_14 0
*M_2_15 0
*M_2_16 0
*M_2_17 0
data type B
1 37 0 0
*M_1_1 2
*M_1_2 2
*M_1_3 2
*M_1_4 0
*M_1_5 2
*M_1_6 0
*M_1_7 0
*M_1_8 2
*M_1_9 0
*M_1_10 0
*M_1_11 0
*M_1_12 2
*M_1_13 0
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*M_1_15 2
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*M_1_17 2
*M_1_18 0
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*M_1_20 0
*M_2_1 2
*M_2_2 2
*M_2_3 2
*M_2_4 0
*M_2_5 0
*M_2_6 0
*M_2_7 0
*M_2_8 2
*M_2_9 2
*M_2_10 2
*M_2_11 0
*M_2_12 0
*M_2_13 2
*M_2_14 0
*M_2_15 0
*M_2_16 2
*M_2_17 2
data type C
1 37 0 0
*M_1_1 0
*M_1_2 0
*M_1_3 2
*M_1_4 2
*M_1_5 2
*M_1_6 2
*M_1_7 0
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*M_1_9 2
*M_1_10 0
*M_1_11 2
*M_1_12 2
*M_1_13 2
*M_1_14 2
*M_1_15 2
*M_1_16 0
*M_1_17 0
*M_1_18 2
*M_1_19 2
*M_1_20 2
*M_2_1 0
*M_2_2 2
*M_2_3 2
*M_2_4 0
*M_2_5 0
*M_2_6 2
*M_2_7 0
*M_2_8 2
*M_2_9 2
*M_2_10 2
*M_2_11 2
*M_2_12 2
*M_2_13 -
*M_2_14 2
*M_2_15 2
*M_2_16 0
*M_2_17 0
data type D
1 37 0 0
*M_1_1 2
*M_1_2 0
*M_1_3 2
*M_1_4 0
*M_1_5 -
*M_1_6 2
*M_1_7 2
*M_1_8 2
*M_1_9 -
*M_1_10 0
*M_1_11 2
*M_1_12 2
*M_1_13 0
*M_1_14 0
*M_1_15 0
*M_1_16 0
*M_1_17 2
*M_1_18 2
*M_1_19 0
*M_1_20 0
*M_2_1 0
*M_2_2 0
*M_2_3 0
*M_2_4 2
*M_2_5 2
*M_2_6 2
*M_2_7 0
*M_2_8 2
*M_2_9 2
*M_2_10 0
*M_2_11 0
*M_2_12 0
*M_2_13 0
*M_2_14 0
*M_2_15 0
*M_2_16 0
*M_2_17 0
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This dataset is a simulated population with the following structure :
A(1) B(1) C(1) D(1)
\ / \ /
AB(100) CD(100)
\ /
F1(100)
|
F2(100)
|
F3(1000)
It features SNP-like observations encoded as 0, 1, and 2, on all four ancestors and the F3 individuals. About 2% of the data is missing.
The genetic map features two chromosomes respectively 150cM and 120cM long with respectively 20 and 17 markers.
Three traits (t1, t2, t3) are simulated for F3:
- t1 on QTL M_2_14 on chromosome ch2 at 104.61cM, with effects A=20, B=30, C=10, D=0, and a small gaussian noise.
- t2 on QTL M_2_14 on chromosome ch2 at 104.61cM, with effects A=100, B=10, C=0, D=200, and a small gaussian noise.
- t3 on QTL M_2_9 on chromosome ch2 at 52.56cM, with effects A=5, B=3, C=6, D=4, and a small gaussian noise.
The commands to run spell-qtl are :
$ spell-pedigree -wd spell -n demo -p F3-outbred.ped
$ spell-marker -n demo -wd spell -m A:02 F3-outbred_A.gen -m B:02 F3-outbred_B.gen -m C:02 F3-outbred_C.gen -m D:02 F3-outbred_D.gen -m F3:02 F3-outbred_F3.gen -o F3
$ spell-qtl -n demo -wd spell/ -gm F3-outbred.map -p F3 F3-outbred_F3.phen -P auto QTL-detection CIM-
To output the 1-point Parental Origin Probabilities, add -O1 to the spell-marker commandline.
To output the n-point Parental Origin Probabilities, add output-nppop to the spell-qtl commandline.
To run spell-marker multi-threaded, add -mt <number of cores> to the spell-marker commandline.
This dataset is a simulated population with the following structure :
A(1) B(1) C(1)
\ / \ /
F1(1) F1C(1)
| |
F2(100) F2C(100)
The genetic map features two chromosomes respectively 150cM and 120cM long with respectively 20 and 17 markers.
One trait (t1) is simulated for F2 and F2C, affected by two QTLs:
- one on chromosome 1 on marker M_1_4 at 14.97cM, with effects A=1, B=0, C=-1, and gaussian noise with parameters (mu=0, sigma=2)
- one on chromosome 2 on marker M_2_6 at 68.37cM, with effects A=1, B=0, C=-1, and gaussian noise with parameters (mu=0, sigma=1)
The commands to run spell-qtl are :
$ spell-pedigree -wd spell/ -n demo -p example1.ped
$ spell-marker -n demo -wd spell -m F2:A/B example1_F2.gen -m F2C:A/C example1_F2C.gen -o F2,F2C
$ spell-qtl -n toto -wd spell -p F2 example1_F2.phen -p F2C example1_F2C.phen -gm example1.map -P auto QTL-detection CIM connected
The connected parameter forces spell-qtl to consider A as the same ancestor in F2 and F2C. You can remove this parameter and see the difference in the final model.
To output the 1-point Parental Origin Probabilities, add -O1 to the spell-marker commandline.
To output the n-point Parental Origin Probabilities, add output-nppop to the spell-qtl commandline.
To run spell-marker multi-threaded, add -mt <number of cores> to the spell-marker commandline.
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