Recent changes to RandomSNPsWMode

RandomSNPsWMode modified by Christos Vlachos

Christos Vlachos — Tue, 03 Jul 2018 10:16:39 -0000

--- v12
+++ v13
@@ -1,6 +1,6 @@
 [TOC]
 #1 Introduction
-We provide a SNP that allows to randomly pick the targets of selection for the w-mode. As input the MimicrEE2 haplotypes are required.
+We provide a SNP that allows to randomly picking the targets of selection for the w-mode. As input the MimicrEE2 haplotypes are required.
 The script provides two options

  * all selected SNPs may have the same effect size
@@ -23,7 +23,7 @@
 * --h the heterozygous effect of the selected SNPs; default = 0.5 
 * --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--s* or *--h*)

-The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as the beneficial one. 
+The script will first select all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Then it selects the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as the beneficial one. 

 #2 Pick SNPs with identical effect size

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:10:53 -0000

--- v11
+++ v12
@@ -64,7 +64,7 @@
 #3 Pick SNPs with an effect size drawn from a distribution

 ## distribution of effect size
-You have to provide a file containing the distribution of effect sizes. 
+To obtain selected SNPs with effect sizes following a distribution you have to provide a file containing the desired distribution of effect sizes. 

 The file needs to have two column and may have an arbitrary number of rows:

@@ -87,7 +87,7 @@

 The script will assign a random effect sizes to each selected SNPs. The effect size is  drawn from this file by picking random rows with replacement.
 Thus the  combination of selection coefficient and heterozygous effect as provided in the file will be maintained.  
-Based on this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.
+Based on this example most SNPs will have a selection coefficient of 0.1 and few will have a selection coefficient of 0.2 or 0.3.  However, all SNPs will have a heterozygous effect of 0.5.

 ## pick the loci

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:06:36 -0000

--- v10
+++ v11
@@ -6,7 +6,7 @@
  * all selected SNPs may have the same effect size
  * the selected SNPs may follow a distribution of effect sizes as provided in a file

-**Note** this is quite similar to randomly picking the targets of selection for the w-mode [RandomSNPsQTL]
+**Note** this is quite similar to randomly picking QTLs for the qt-mode and the qff-mode [RandomSNPsQTL]

 ## Requirements

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:06:05 -0000

--- v9
+++ v10
@@ -5,6 +5,8 @@

  * all selected SNPs may have the same effect size
  * the selected SNPs may follow a distribution of effect sizes as provided in a file
+
+**Note** this is quite similar to randomly picking the targets of selection for the w-mode [RandomSNPsQTL]

 ## Requirements

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 15:16:01 -0000

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 15:15:49 -0000

--- v7
+++ v8
@@ -20,6 +20,8 @@
 * --s the selection coefficients of the selected SNPs (either --s or --effect-file needs to be provided) 
 * --h the heterozygous effect of the selected SNPs; default = 0.5 
 * --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--s* or *--h*)
+
+The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as the beneficial one.

 #2 Pick SNPs with identical effect size

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 14:43:49 -0000

--- v6
+++ v7
@@ -10,7 +10,7 @@
 ## Requirements
 First download the MimicrEE2 haplotypes https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download

-Than download the script
+Than download the script https://sourceforge.net/projects/mimicree2/files/scripts/pick-SNPs-selcoef.py/download

 the following parameters are important:

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 14:40:37 -0000

--- v5
+++ v6
@@ -81,9 +81,9 @@
 ~~~~~

-The script will assign a random effect sizes to each selected SNPs. The effect size is randomly drawn from this file by picking random rows with replacement.
-Thus the combination of selection coefficient and heterozygous effect provided in this file will be maintained.  
-For this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.
+The script will assign a random effect sizes to each selected SNPs. The effect size is  drawn from this file by picking random rows with replacement.
+Thus the  combination of selection coefficient and heterozygous effect as provided in the file will be maintained.  
+Based on this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.

 ## pick the loci

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 14:39:03 -0000

--- v4
+++ v5
@@ -81,14 +81,43 @@
 ~~~~~

-The script will assign a random effect size from this file to each of the selected SNPs (basicall it draws random rows, thus the combination of selectio coefficient and heterozygous effect will be maintained).  For this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.
+The script will assign a random effect sizes to each selected SNPs. The effect size is randomly drawn from this file by picking random rows with replacement.
+Thus the combination of selection coefficient and heterozygous effect provided in this file will be maintained.  
+For this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.

 ## pick the loci
+
 With the following command we randomly pick the loci

 ~~~~~
 python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05
+~~~~~
+
+and we obtain an output similiar to this one
+
+~~~~~
+[s]
+3R 6941048 C/T 0.1 0.5
+2R 12592831    C/G 0.1 0.5
+3L 8315781 T/G 0.5 0.5
+2L 15620577    T/C 0.5 0.5
+3R 9870974 C/T 0.5 0.5
+3R 7009549 T/A 0.5 0.5
+3L 14816601    A/C 0.1 0.5
+2R 19007146    G/A 0.5 0.5
+2R 10030750    C/T 0.3 0.5
+3L 12571197    C/T 0.1 0.5
+3L 10579497    T/C 0.2 0.5
+2L 17368433    T/A 0.3 0.5
+3L 12988113    C/T 0.1 0.5
+X  13161667    A/C 0.1 0.5
+2L 2719442 T/C 0.3 0.5
+3R 14201605    T/A 0.1 0.5
+2R 10250433    C/A 0.4 0.5
+2R 9251683 C/G 0.1 0.5
+3R 21063725    C/A 0.4 0.5
+2L 11212417    G/A 0.2 0.5
 ~~~~~

@@ -97,3 +126,4 @@

+

RandomSNPsWMode modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 14:30:33 -0000

--- v3
+++ v4
@@ -7,8 +7,7 @@
  * the selected SNPs may follow a distribution of effect sizes as provided in a file

-# Pick SNPs with identical effect size
-
+## Requirements
 First download the MimicrEE2 haplotypes https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download

 Than download the script
@@ -18,8 +17,13 @@
 * --mimhap the MimicrEE2 haplotype file; may be zipped or unzipped
 * --n the number of selected loci
 * --f the minimum allele frequency; For example if *--f 0.05* is provided all SNPs will have an allele frequency betwee 0.05 and 0.95
-* --s the selection coefficients of the selected SNPs
-* --h the heterozygous effect of the selected SNPs 
+* --s the selection coefficients of the selected SNPs (either --s or --effect-file needs to be provided) 
+* --h the heterozygous effect of the selected SNPs; default = 0.5 
+* --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--s* or *--h*)
+
+#2 Pick SNPs with identical effect size
+
+

 ~~~~~~
 python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --s 0.1 --f 0.05 > sellocus.txt
@@ -51,5 +55,45 @@
 3R 634316  C/T 0.1 0.5
 ~~~~~

+For details on this file format see [SelectedLoci]
+
+#3 Pick SNPs with an effect size drawn from a distribution
+
+## distribution of effect size
+You have to provide a file containing the distribution of effect sizes. 
+
+The file needs to have two column and may have an arbitrary number of rows:
+
+* column1: the selection coefficient
+* column2: the heterozygous effect

+For examle given the following content stored in file *effectsizedistr.txt*
+~~~~~
+0.1     0.5
+0.1     0.5
+0.1     0.5
+0.1     0.5
+0.2     0.5
+0.3     0.5
+0.4     0.5
+0.5     0.5
+~~~~~
+
+
+The script will assign a random effect size from this file to each of the selected SNPs (basicall it draws random rows, thus the combination of selectio coefficient and heterozygous effect will be maintained).  For this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.
+
+
+## pick the loci
+With the following command we randomly pick the loci
+
+~~~~~
+python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05
+~~~~~
+
+
+
+
+
+
+