First, I just want to thank you for answering my previous inquiry,
I have a little confusion that I do hope you would clarify for me, please?
In your paper, I have read the following paragraph:
When the rate of EHH decay is similar on the ancestral and
derived alleles, iHHA/iHHD ’ 1, and hence the unstandardized
iHS is ’ 0. Large negative values indicate unusually
long haplotypes carrying the derived allele; large positive
values indicate long haplotypes carrying the ancestral allele.
So, using the example data, I have tried to plot both snp with extreme values (the highest negative and positive value as well snp with iHS zero value.
Hi dear,
First, I just want to thank you for answering my previous inquiry,
I have a little confusion that I do hope you would clarify for me, please?
In your paper, I have read the following paragraph:
When the rate of EHH decay is similar on the ancestral and derived alleles, iHHA/iHHD ’ 1, and hence the unstandardized iHS is ’ 0. Large negative values indicate unusually long haplotypes carrying the derived allele; large positive values indicate long haplotypes carrying the ancestral allele.
So, using the example data, I have tried to plot both snp with extreme values (the highest negative and positive value as well snp with iHS zero value.
This plot produced from locus with the highest iHS value which according to the above paragraph, I am expecting to see extended ancestral allele. However, I do see the opposite (extended derived allele) https://www.dropbox.com/s/aa5lu2wsw0rpl58/example.Locus5138.ehh.Locus5138.out.ehh.eps?dl=0
This plot for iHS with the highest negative value. Similarly, I do see extended derived allele not vice versa. https://www.dropbox.com/s/7zmj8ro3o49rqcb/example.Locus6691.ehh.Locus6691.out.ehh.eps?dl=0
This plot for snp with nearly zero iHS value https://www.dropbox.com/s/azilt4kjh09szhw/example.Locus3712.ehh.Locus3712.out.ehh.eps?dl=0
I would much appreciate if you could explain this,
Thanks
Salha