I'm quite new to population genetics and recently looked at these papers and found that the negative values in kinship matrix are switched to zeros.
https://www.nature.com/articles/srep41561
The relative kinship matrix comparing all pairs of accessions was calculated using the software package SPAGeDi. Negative values between two individuals were set to 0
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405135/pdf/fpls-08-00593.pdf
The relative kinship matrix (K matrix) was obtained using SPAGeDi , and negative values between two rapeseed accessions were set to 0.
both articles then cite: "A unified mixed-model method for association mapping that accounts for multiple levels of relatedness" by Yu who then cite "SPAGeDI: A versatile computer program to analyze spatial genetic structure at the individual or population levels" by Hardy.
This a bit confusing and I still can't find an explanation.
Is this is just a common convention? And in case if I use TASSEL to make kinship matrix by Centered IBS method which produces negative values, should I switch them to zeros too?
Thanks! But still it is not clear why kinship matrix produced by Tassel contains negative values as well as why this values not in range from 0 to 1 i.e. there are numbers that are actually larger than 1. If someone could explain It would be great. Unfortunately I didn't find the relevant explanation in Tassel's manual.
Done some more reading and felt like I should update my answer. I found this paragraph in Spagedi manual:
So there are two terms, sometimes used without distinction. The procedure to set negative values as zeros was specifically written in Yu et al mixed model paper:
The developers of EMMA say it's a bad idea because the kinship matrix "may not be positive semidefinite and thus might not be a valid form of variance component"