[Sysgensim-users] Specifying parameter values

[Priya A. <gal...@ya...>]

Hi,I have started using sysgensim to simulate expression data and have some queries in specifying the genetic parameters. I used the default value specified for each parameter and generated expression values. Otherwise, when do I change these parameter values? For example, there are 2 outliers in the expression value of one gene. So do I have to change the value of SD in transcriptional variance and degradation variance and simulate till the expression values of this gene across all the subjects are within the same range? How do I decide on setting the mean and SD values for cooperativity coefficient, transcriptional and degradation variance?. Please guide me on this issue.
In the genotype matrix file, genes are given either values 0 or 1. Does 0 mean, it is a minor allele and 1 mean it is a major allele?. As upper and lower bound values for Z are given, value between the lower bound and upper bound becomes 1 and value lower than lower bound becomes 0?
Thank youRegardsPriya