change count thresholds to be fractions instead of integers

[kelly-sovacool]

previously, ccbrpipeliner used fractions which was more portable across groups of different sizes.

current code straight from nidap:
https://github.com/CCBR/reneeTools/blob/79e612e588083869d139dd497f480676dda280bc/R/filter.R#L247-L300

[kelly-sovacool]

@phoman14 do you have any thoughts on this?

[phoman14]

do you mean that if a dataframe has 14 samples then Minimum_Number_of_Samples_with_Nonzero_Counts_in_Total = 0.5 instead of Minimum_Number_of_Samples_with_Nonzero_Counts_in_Total = 7?

[kelly-sovacool]

do you mean that if a dataframe has 14 samples then Minimum_Number_of_Samples_with_Nonzero_Counts_in_Total = 0.5 instead of Minimum_Number_of_Samples_with_Nonzero_Counts_in_Total = 7?

Yes exactly. This is @kopardev's suggestion.

[phoman14]

I think this is a fine way to do it.
In my head It is easier to specify the exact number but if we make the input a fraction we could always calculate the fraction upstream from the exact number.
The other consideration is the input format. We should include an error check to make sure the input is in the correct format. I could see a user not understanding the format in enter any of the following 0.5, 50% or 50