README.QPGRAPH

qpGraph -p parfile -g graph [-o outgraph] [-d dotfile] 

See examples/runit for some simple examples and sample output

Sample parameter file
DIR:   ../data
S1:              sim1           
indivname:       DIR/S1.ind  
snpname:         DIR/S1.snp       
genotypename:    DIR/S1.geno  
outpop:         Out     
blgsize:        0.05
## block size in Morgans for Jackknife
## see below 
lsqmode:       YES
diag:          .0001
hires:         YES
initmix:      1000 
precision:    .0001  
zthresh:      3.0
terse:        NO
useallsnps:   NO


-p parfile specifies input data (any Reich lab format) 

outpop:   zzz
f-stats normalized by heterozygosity in population zzz 
outpop:  NULL  has special meaning : no normalization 
blgsize: block size for Jackknife (Morgans)
lsqmode:   Default is NO;  Estimate of error covariance is used.  Unstable for large problems 
 and instead we fit f_3 stats with "base" population first label (see graph spec)
diag:   small fudge factor to add on diagonal of f3.  Improves stability
Given admixing weights the edge lengths (drifts) are set by minimizing 
a degree 2 function, subject to non-negativity of the lengths.  
Initially the program tries V initial tries of admixing weights 
defailt value for V is 10 . 2^n where there are n admixtures in the graph. 
To override this default

initmix:   V  
where V is the desired number of initial tries.  This may be useful 
if you are worried the program may not have found the global optimum. 

hires:   controls output sometimes more decimals are desired
precision:  controls accuracy of recovereed admixture weights.  Coefficients will be within "precision" of MLE estimate.
zthresh: controls outlier output.  All f-stats are calculated and those diverging more then "zthresh" from fitted values 
 printed.e all SNPs even if some populations hav e n data for a SNP (default NO) 

-g graph  
See examples.qpGraph/gr1x 
Note comments can be included in file. Begin a line with #

[-o outgraph]  This can be hand edited and input again.  Note format is different. 
qpGraph will accept either style.  

[-d dotfile]  Graph output in "dot format";  dot -Tps < dotfile > dotfile.ps gives postscript
"dot" must be installed (part of Graphviz) 

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Utility program: qpreroot
If the input graph is not connected or has loops qpGraph will die unpleasantly.  
Best way to see what is happening: 

qpreroot -g graph -d dotfile  
## This also makes postscript

We also can change the root node 
qpreroot -g graph -o outgraph -r node