Recent changes to QTPolygenicSimu

QTPolygenicSimu modified by Guobo Chen

Guobo Chen — Tue, 28 Apr 2015 22:54:28 -0000

--- v3
+++ v4
@@ -23,16 +23,16 @@
 **--freq-file**
 **Specify the file which contains frequency for the reference alleles. One element per line.**

---effect <arg>
-Specify the effect of for loci. 0.5 by default.
-
 --poly-effect
-It generates polygenic effect from N(0,1).
+It generates polygenic effects from the standard normal distribution.

 --poly-effect-sort
-It generates sorted polygenic effects from N(0,1).
+It generates polygenic effects from the standard normal distribution.  Different from --poly-effect, this option will sort the genetic effects in ascending order to the markers, say the first marker has the smallest effect and the last the biggest.

---effect-file
+--effect <arg>
+Specify the universal effect of each loci. 0.5 by default.
+
+--effect-file <arg>
 Specify the file which contains the effects for each locus.

 --ld <arg>

QTPolygenicSimu modified by Guobo Chen

Guobo Chen — Tue, 28 Apr 2015 22:48:44 -0000

--- v2
+++ v3
@@ -35,11 +35,11 @@
 --effect-file
 Specify the file which contains the effects for each locus.

-**--ld <arg>**
-Specify LD in Lewontin's D'. 0 by default.
+--ld <arg>
+Specify LD in Lewontin's D', a value between -1 to 1. 0 by default.

-**--rand-ld**
-It generates Lewontin's D' from uniform distribution between -1,1.
+--rand-ld
+It generates Lewontin's D' from the uniform distribution between -1,1.

 --hsq <arg>
 Specify the heritability. 0.5 by default.
@@ -55,3 +55,8 @@
 gear simuqt --n 1000 --m 1000 --freq-file frq.txt --poly-effect --ld 0.8 --out test
 ~~~~~

+The output files includes
+*.phe: there are four columns included. The first two columns are family id, and individual id. The 3rd column is genotypic values (breeding values), and the 4th column is phenotypic values.
+*.rnd: there are three columns included. 1st is the marker name, 2nd is the reference alleles, the 3rd column is additive effects.
+*.add: the genotype in additive model coding scheme.
+*.bim, *.fam, *.bed: the genotype in plink binary format.

QTPolygenicSimu modified by Guobo Chen

Guobo Chen — Sun, 28 Dec 2014 06:09:01 -0000

--- v1
+++ v2
@@ -49,9 +49,9 @@

 Examples

-~~~
+~~~~~
 gear simuqt --n 1000 --m 1000 --null-loci 900 --freq 0.45 --ld 0.3 --hsq 0.25 --poly-effect --out test
 gear simuqt --n 1000 --m 1000 --null-loci 500 --unif-freq --rand-ld --hsq 0.2 --effect-file eff.txt --out test
 gear simuqt --n 1000 --m 1000 --freq-file frq.txt --poly-effect --ld 0.8 --out test
-~~~
+~~~~~

QTPolygenicSimu modified by Guobo Chen

Guobo Chen — Sat, 27 Dec 2014 13:14:54 -0000

Simulation for polygenic quantitative traits

Master option
simuqt

Options
--sample-size/--n
Specify the sample size. 100 by default.

--marker/--m
Specify the number of total markers. 100 by default.

--null-marker
Specify the number of markers from null distribution. 0 by default.

--freq <arg>
Specify the frequencies for the markers. 0.5 by default.

--unif-freq
It generates frequency spectrum from uniform distribution between 0.01~0.5.

--freq-file
Specify the file which contains frequency for the reference alleles. One element per line.

--effect <arg>
Specify the effect of for loci. 0.5 by default.

--poly-effect
It generates polygenic effect from N(0,1).

--poly-effect-sort
It generates sorted polygenic effects from N(0,1).

--effect-file
Specify the file which contains the effects for each locus.

--ld <arg>
Specify LD in Lewontin's D'. 0 by default.

--rand-ld
It generates Lewontin's D' from uniform distribution between -1,1.

--hsq <arg>
Specify the heritability. 0.5 by default.

--make-bed
It generates genotypes in bed format.

Examples

~~~
gear simuqt --n 1000 --m 1000 --null-loci 900 --freq 0.45 --ld 0.3 --hsq 0.25 --poly-effect --out test
gear simuqt --n 1000 --m 1000 --null-loci 500 --unif-freq --rand-ld --hsq 0.2 --effect-file eff.txt --out test
gear simuqt --n 1000 --m 1000 --freq-file frq.txt --poly-effect --ld 0.8 --out test
~~~