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gxiaolab / cGMAS

Concordance-based approach for prediction of functional SNPs for GMAS
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Concordance score calculation #2

Open CharlesAnalyst opened 3 years ago

CharlesAnalyst commented 3 years ago

hi, i am very interested in calculation of "concordance score". However, in my attempt to understand how it reasoned, i got stuck. Especially, when determining whether it is closer to 1 or closer to 0. And what exactly is the role of the "prominent peaks" in this process.

i would appreciate it if you could reply to me. Thanks, Charles

kofiamoah commented 3 years ago

Hi @CharlesAnalyst, I am so sorry for the late reply. My github account was associated with an email address that I no longer use so I never got a notification. The concordance score is essentially a measure of how much correspondence there is between a SNV genotype and imbalance in an alternatively spliced region. And for each candidate SNP, the peak refers to the density of samples/individuals in which the given SNV has that score. So a stronger at or peak closer to 1 is probably more functional than one closer to zero