Recent changes to SimuFamily

SimuFamily modified by Guobo Chen

Guobo Chen — Sun, 28 Dec 2014 23:44:08 -0000

--- v11
+++ v12
@@ -1,8 +1,9 @@
 ##Simulation for nuclear family##
 ------------------------
-It is a very naive simulation for discordant nuclear sib-pair families.  Equi-biallelic loci are simulated for discordant family.
+This procedure helps generate nuclear families, having two parents and a pair of children.

-**Subcommand: ** simufam
+**Subcommand: ** 
+simufam

 **Available Options**
 -f, --num-fam <arg>
@@ -11,7 +12,7 @@
 -m, --num-marker <arg>
 Specify the number of markers.

--s,--seed <arg>
+-s, --seed <arg>
 Specify the seed of random number generator.

 --make-bed
@@ -21,10 +22,10 @@
 Specify the output root filename

 --freq <arg>
-Specify the maf for simulation. By default, maf = 0.5.
+Specify the allelic frequency for simulation. By default, freq = 0.5 for all loci.

 --unif-freq
-Randomly generate maf in a uniform distribution from 0.01 to 0.5.
+Randomly generate allelic frequency in a uniform distribution from 0.01 to 0.5.

 --rec <arg>
 Specify a universal recombination fraction, which is applied to the genome.
@@ -37,6 +38,9 @@

 --ld <arg>
 Specify a universal ld (in DPrime). By defaulty, ld = 0.
+
+--rand-ld
+Generates ld from the uniform distribution from -1 to 1.

 **Examples**

SimuFamily modified by Guobo Chen

Guobo Chen — Sun, 28 Dec 2014 05:27:06 -0000

--- v10
+++ v11
@@ -14,35 +14,48 @@
 -s,--seed <arg>
 Specify the seed of random number generator.

--b,--make-bed
+--make-bed
 If this option is set, then .bed, .bim and .fam files will be outputted; otherwise .ped and .map files will be outputted.

--o,--out <arg>
+--out <arg>
 Specify the output root filename

---maf <arg>
+--freq <arg>
 Specify the maf for simulation. By default, maf = 0.5.

--mr, --maf-rand
+--unif-freq
 Randomly generate maf in a uniform distribution from 0.01 to 0.5.

--r, --rec <arg>
+--rec <arg>
 Specify a universal recombination fraction, which is applied to the genome.

--rs, --rec-sex <arg>
+--rec-sex <arg>
 Specify a universal recombination fractions for males and females.

--rr, --rec-rand
+--unif-rec
 Randomly generate recombination fractions in a uniform distribution from 0 to 0.5.

--l, --ld <arg>
+--ld <arg>
 Specify a universal ld (in DPrime). By defaulty, ld = 0.

-**Example**
+**Examples**
+
+~~~~~~~~~
+1 Generating 100 nuclear families, and each individual has 100 markers. Allelic frequency is 0.5 for each locus, and loci are in linkage disequilibrium 
 gear simufam --num-fam 100 --num-marker 100 --out poly
-gear simufam -f 100 -m 100 -b -o poly
+
+2 Generating 100 nuclear families, and each individual has 100 markers. Allelic frequency is 0.5, and ld for a pair of neighboring markers is 0.8, and recombination fraction is 0.1
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec 0.1 --out poly
+
+3 Similar to the last simulation, but parents have heterogeneous recombination fractions of 0.1 and 0.2
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-sex 0.1 0.2 --out poly
-gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-rand --make-bed --out poly
-gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --maf 0.3 --make-bed --out poly
-gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --maf-rand --make-bed --out poly
+
+4 Recombination follows uniform distribution
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --unif-rec --make-bed --out poly
+
+5 Allele frequency is 0.3 for each locus
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --freq 0.3 --make-bed --out poly
+
+6 Allele frequency follows uniform distribution between 0.01~0.5
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --unif-freq --make-bed --out poly
+~~~~~~~~~~

SimuFamily modified by Guobo Chen

Guobo Chen — Fri, 26 Dec 2014 12:26:51 -0000

--- v9
+++ v10
@@ -42,7 +42,7 @@
 gear simufam --num-fam 100 --num-marker 100 --out poly
 gear simufam -f 100 -m 100 -b -o poly
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec 0.1 --out poly
-gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-sex 0.1,0.2 --out poly
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-sex 0.1 0.2 --out poly
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-rand --make-bed --out poly
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --maf 0.3 --make-bed --out poly
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --maf-rand --make-bed --out poly

SimuFamily modified by Guobo Chen

Guobo Chen — Thu, 30 Jan 2014 12:09:34 -0000

--- v8
+++ v9
@@ -36,7 +36,7 @@
 Randomly generate recombination fractions in a uniform distribution from 0 to 0.5.

 -l, --ld 
-Specify a universal ld (in DPrime).
+Specify a universal ld (in DPrime). By defaulty, ld = 0.

 **Example**
 gear simufam --num-fam 100 --num-marker 100 --out poly

SimuFamily modified by Guobo Chen

Guobo Chen — Mon, 27 Jan 2014 11:30:02 -0000

--- v7
+++ v8
@@ -20,6 +20,12 @@
 -o,--out 
 Specify the output root filename

+--maf 
+Specify the maf for simulation. By default, maf = 0.5.
+
+-mr, --maf-rand
+Randomly generate maf in a uniform distribution from 0.01 to 0.5.
+
 -r, --rec 
 Specify a universal recombination fraction, which is applied to the genome.

@@ -38,3 +44,5 @@
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec 0.1 --out poly
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-sex 0.1,0.2 --out poly
 gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-rand --make-bed --out poly
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --maf 0.3 --make-bed --out poly
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --maf-rand --make-bed --out poly

SimuFamily modified by Guobo Chen

Guobo Chen — Sat, 25 Jan 2014 07:41:31 -0000

--- v6
+++ v7
@@ -5,11 +5,11 @@
 **Subcommand: ** simufam

 **Available Options**
--f,--num-fams 
+-f, --num-fam 
 Specify the number of families.

--m,--num-markers 
-Specifiy the number of markers.
+-m, --num-marker 
+Specify the number of markers.

 -s,--seed 
 Specify the seed of random number generator.
@@ -33,8 +33,8 @@
 Specify a universal ld (in DPrime).

 **Example**
-gear simufam --num-fams 100 --num-markers 100 --out poly
+gear simufam --num-fam 100 --num-marker 100 --out poly
 gear simufam -f 100 -m 100 -b -o poly
-gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec 0.1 --out poly
-gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec-sex 0.1,0.2 --out poly
-gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec-rand --make-bed --out poly
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec 0.1 --out poly
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-sex 0.1,0.2 --out poly
+gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-rand --make-bed --out poly

SimuFamily modified by Guobo Chen

Guobo Chen — Sat, 25 Jan 2014 07:40:30 -0000

--- v5
+++ v6
@@ -23,6 +23,9 @@
 -r, --rec 
 Specify a universal recombination fraction, which is applied to the genome.

+-rs, --rec-sex 
+Specify a universal recombination fractions for males and females.
+
 -rr, --rec-rand
 Randomly generate recombination fractions in a uniform distribution from 0 to 0.5.

@@ -33,4 +36,5 @@
 gear simufam --num-fams 100 --num-markers 100 --out poly
 gear simufam -f 100 -m 100 -b -o poly
 gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec 0.1 --out poly
+gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec-sex 0.1,0.2 --out poly
 gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec-rand --make-bed --out poly

SimuFamily modified by Guobo Chen

Guobo Chen — Sat, 18 Jan 2014 03:22:26 -0000

--- v4
+++ v5
@@ -20,6 +20,17 @@
 -o,--out 
 Specify the output root filename

+-r, --rec 
+Specify a universal recombination fraction, which is applied to the genome.
+
+-rr, --rec-rand
+Randomly generate recombination fractions in a uniform distribution from 0 to 0.5.
+
+-l, --ld 
+Specify a universal ld (in DPrime).
+
 **Example**
 gear simufam --num-fams 100 --num-markers 100 --out poly
 gear simufam -f 100 -m 100 -b -o poly
+gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec 0.1 --out poly
+gear simufam --num-fams 100 --num-markers 100 --ld 0.8 --rec-rand --make-bed --out poly

SimuFamily modified by Guobo Chen

Guobo Chen — Sat, 11 Jan 2014 11:14:13 -0000

--- v3
+++ v4
@@ -8,7 +8,7 @@
 -f,--num-fams 
 Specify the number of families.

--m,--num-fams 
+-m,--num-markers 
 Specifiy the number of markers.

 -s,--seed 
@@ -21,5 +21,5 @@
 Specify the output root filename

 **Example**
-gear simufam --num-fams 100 --num-fams 100 --out poly
+gear simufam --num-fams 100 --num-markers 100 --out poly
 gear simufam -f 100 -m 100 -b -o poly

SimuFamily modified by Zhixiang Zhu

Zhixiang Zhu — Sat, 21 Sep 2013 17:10:58 -0000

--- v2
+++ v3
@@ -1,21 +1,25 @@
-
 ##Simulation for nuclear family##
 ------------------------
-It is a very naive simulation for discordant nuclear families.  Equi-biallelic loci are simulated for discordant family.
+It is a very naive simulation for discordant nuclear sib-pair families.  Equi-biallelic loci are simulated for discordant family.

-**Master command**
---simu-fam
-The master option to simulate nuclear discordant sib-pair families.
+**Subcommand: ** simufam

---simu-fam-size
+**Available Options**
+-f,--num-fams 
 Specify the number of families.

---simu-fam-marker
+-m,--num-fams 
 Specifiy the number of markers.

---simu-seed
-Specify the seed for simulation.
+-s,--seed 
+Specify the seed of random number generator.

-Example
-gear --simu-fam --simu-fam-size 100 --simu-fam-marker 100 --out poly
-gear --simu-fam --simu-fam-size 100 --simu-fam-marker 100 --make-bed --out poly
+-b,--make-bed
+If this option is set, then .bed, .bim and .fam files will be outputted; otherwise .ped and .map files will be outputted.
+
+-o,--out 
+Specify the output root filename
+
+**Example**
+gear simufam --num-fams 100 --num-fams 100 --out poly
+gear simufam -f 100 -m 100 -b -o poly