I am using MapQTL5 to identify the QTL and now like to calculate R^2t. If some one knows how to do it or has any good software to suggest. Please share. Thanks
The percentage of total variation in marker association for each trait across population explained by QTL is equivalent to R2 explained by linear regression.
QTL cartographer can also be used to calculate R2 depending on methods used. Again it will vary with single factor analysis of variance, simple interval mapping, composite interval mapping and multiple interval mapping
I am using MapQTL6. You can also use Simple interval mapping and MQM mapping to calculate R2 (percentage of explained phenotypic variance for the trait by marker) in MapQTL5 software.
Do you want to calculate R2 of the model or you want to calculate the partial R2 (markers associated with QTL)? For the first case you can divide the sum of squares of the model by the total sum of squares. You can always also square the correlation coefficient between the two variables you are interested in, say: r(x,y)=(Cov(x,y))/sqroot(Var(x)*Var(y))and squared this value. Or you can simply take r2=Var(marker)/Var(phenotypic).
I hope this help!!!
IF i am right your mean is R2 total which you must sum up all R2 from the putative qtl and report as the amount of phenotype variation explained by all qtls
I calculatet R^2 via the lm function in R. I examined how differences in my quantitative trait can be explained by differences in the diplotype effect (calculated via ASReml). It resulted in 0.58 for R^2. Or in case of the multiple linear regression (Diplotype effect, age, sex, body weight and height) 0.77. I would like to ask how to interpret these values in my discussion. How good are these values and how much i can trust them. Please advice me some good literature.
Thanks in advance
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