I have couple of queries regarding QTL (Enzyme activity) association with genotypes which I did and I am a novice in this field
First one is regarding the Plink output file generated using --qassoc command for quantitative trait for unphased genotypes. ( --qassoc gives allelic association (I presume)?). Is there a program by which i can check genotypic association with a quantitative trait?(there is genotypic means in plink but it doesn't give a Pvalue). I was able to get significant P values but was not able to find what is the significance of Beta, SE, R2 and T values. Would any of these parameters help to say the percentage of variance in the quantitative trait explained due to the presence of a particular variant?
I have also generated sliding window haplotypes for association with quantitative trait(4 marker & 6 marker)? What is the basis for window size determination(I have a total of 64 markers spanning 22kb)? and what does BETA, R2, STAT and PS in the output format signify. Is there a method by which we can estimate the haplotypic means for quantitative trait for the associated haplotypes?
Would you pls help me with this queries