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mehrnoushmalek / flowDensity

Automated gating
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singlet.gate doesn't seem to be mentioned anywhere except the docs #1

Closed nicbarker closed 6 years ago

nicbarker commented 6 years ago

Hi, In the vignettes, there is an example that mentions the following:

sglt <- flowDensity(obj=lymph, singlet.gate=TRUE)

On my machine, this throws an error:

> sglt <- flowDensity(obj=lymph, singlet.gate=TRUE)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘flowDensity’ for signature ‘"CellPopulation", "missing", "missing", "missing"’

When I grep the codebase, there doesn't seem to be any mention of singlet.gate except for in the documentation.

Is there something I'm missing here?

mehrnoushmalek commented 6 years ago

I got rid of singlet.gate as it depends on a sample, but haven't had time to update the man page. I'm away, but will look into it first thing next week. If you want to remove singlets, I suggest doing: Sngl<- flowDensity(frame, c( "FSC-A", "SSC-A"), c( F,F), use.percentile=c(T, T), percentile=c( .99,.99), scale=.98)

You need to play with scale and percentile to get what you want.

nicbarker commented 6 years ago

Thanks for the tip! This isn't the highest priority issue, just thought I'd point it out.