Latest revision as of 23:13, 25 January 2018

ms and psmc stuff

./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l

N0=theta/regionsize/4/u

30000.0/30000000.0/4.0/u=10000

from ms to realtime and realsize

tk are times from ms e.g. 0.01,0.06,0.2,1,2

alpha are sizes from ms e.g. 0.1,1,0.5,1,2

truetimes in years

4*g*N0*tk

from ms to real populationsize

alpha*N0

from psmc to realtime and realsize:

PA 4+25*2+4+6 0.026254885 0.003600825 21.895293401 5.782425186 2.106578468 0.452471596 0.479814497 0.401498376 0.367130222 0.302637758 0.336141050 0.585819704 1.405835053 2.909550136 4.044915857 4.137850214 3.776532973 3.123633638 2.466466904 2.013826351 1.792827385 1.762345431 1.839956170 1.916823191 1.921452795 1.902858530 2.051184729 2.597031978 3.508703366 4.125487051 6.375234256

Theta is third value.

N0=theta/2/u/s

from psmc time to realtime

2*g*N0*times

from psmc time to realtime

N0*lambda

Wiki doc

check userdir is writable
write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
user custom class missing

Code fix/cleanup

if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
don't quit program if a chr is not included in the -sites file
check all getoptions stderr output.
from morten shitoutput

h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 11 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1…

Addtional methods and functionality

make haploid 1dsfs
simplefy filereading. from glf files
fix -doFasta for single chromosomes.

User:Thorfinn: Difference between revisions

Latest revision as of 23:13, 25 January 2018

Contents

ms and psmc stuff

Wiki doc

Code fix/cleanup

Addtional methods and functionality

Navigation menu

@@ Line 1: / Line 1: @@
-Thorfinns angsd todolist
+=ms and psmc stuff=
+./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l
-) write error estimation on wiki, need more info
+N0=theta/regionsize/4/u
-)
+.0/30000000.0/4.0/u=10000
+from ms to realtime and realsize
+tk are times from ms e.g. 0.01,0.06,0.2,1,2
+alpha are sizes from ms e.g. 0.1,1,0.5,1,2
+truetimes in years
+*g*N0*tk
+from ms to real populationsize
+alpha*N0
+from psmc to realtime and realsize:
+PA	4+25*2+4+6 0.026254885 0.003600825 21.895293401 5.782425186 2.106578468 0.452471596 0.479814497 0.401498376 0.367130222 0.302637758 0.336141050 0.585819704 1.405835053 2.909550136 4.044915857 4.137850214 3.776532973 3.123633638 2.466466904 2.013826351 1.792827385 1.762345431 1.839956170 1.916823191 1.921452795 1.902858530 2.051184729 2.597031978 3.508703366 4.125487051 6.375234256
+Theta is third value.
+N0=theta/2/u/s
+from psmc time to realtime
+*g*N0*times
+from psmc time to realtime
+N0*lambda
+=Wiki doc=
+#  check userdir is writable
+# write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
+#user custom class missing
+=Code fix/cleanup=
+#if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
+# don't quit program if a chr is not included in the -sites file
+#check all getoptions stderr output.
+# from morten shitoutput
 <pre>
-Rscript ../../angsd0.565/R/estError.R
+h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
-Loading required package: remix
+h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
-Loading required package: plyr
+h1 h2 h3 = 10 11 5  has less than 3 blocks. skipping
-Loading required package: survival
+h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
-Loading required package: splines
+h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
-Warning message:
+h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
-no function found corresponding to methods exports from ‘ascii’ for: ‘show’
+h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
-->  needed arguments:
+h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
-	 file : the ancError File
+h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
-->  optional arguments (defaults):
+h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
-	 out  ( errorEst ) : Name of the out files
+h1…
-	 indNames  ( ind ) : postFix, file with names or comma seperated names of individuals
-	 nIter  ( 100 ) : Numer of optimazation attemps
-	 subset  ( NA ) : comma seperated numbers of the individuals to include
-	 main  ( Error rate using an outgroup (Chimp) and a perfect man ) :
-	 maxErr  ( 0.02 ) : maximum allowed error rate
-	 height  ( 7 ) : height of the pdf
-	 width  ( 11 ) : width of the pdf
-	 cex  ( 1 ) : scale of names
 </pre>
-. -filter to site
-. add single pars
+=Addtional methods and functionality=
+# make haploid 1dsfs
+# simplefy filereading. from glf files
+# fix -doFasta for single chromosomes.