Scout: Local observations visualization displayed as frequencies.

[northwestwitch]

From the notes of the last user meeting (#1679)

[northwestwitch]

@mikaell this one perhaps. It's about converting the loqus db observations in the same format as the other frequencies.

[mikaell]

Ok. Already I'll start looking into this.

[mikaell]

This is my proposed implementation -add an extra entry in the Frequencies table.

How are frequencies calculated? (@dnil)

[northwestwitch]

When you find out what exactly is that number (Total nr.) you could perhaps add a tooltip to the text to clarify what the field is..

[dnil]

Hm, it isn’t supposed to be? Our locals are generally count based. Obviously one can show counts divided by chromosomes seen, but it is not clear that it will converge on population frequency or what the bias will be. If we must, at least show both counts and ratio, possibly via tooltip as C suggest? @moonso is perhaps a non-vacation goto person for local counts? 😊

[mikaell]

Ok, I'll prepare the code infrastructure in the mean time.

[moonso]

Hi, we should not display it as frequencies since they are not frequencies. For example we count a variant only once per family regardless of the number of individuals that holds the variant in that family. For more information about this read the paper 😄

Edit. To be more clear, showing it as a frequency would only be misguiding so I do not think we should do that

[northwestwitch]

For more information about this read the paper

😆

But then problem fixed. Thanks for the explanation @moonso (and congrats for the paper!)