Open madleina opened 9 months ago
As the X chromosome mapping rate can be affected by a variety of factors, we strictly require that the X chromosome mapping rate for XXX be twice that for females (XX). Using a factor of 1.5 is also a viable alternative. The optimal threshold may require additional evaluation.
Hey
I think there is a mistake in the code that classifies XXX samples (seGMM.r, line 106). The first statement is
feature[i,"Xmap"]>(2*mean_f_xmap)
which means that you expect twice as many reads on the X chromosome in XXX compared to females (XX). I think it should rather be 1.5 (XX -> XXX is a factor 1.5). Do you agree with this?