If
CLINSIG has a value in it of Benign, then for the particular line the
Classification is
Benign. So I guess if
CLINSIG has a value in it then that is the
Classification and none of the conditions are applied.
My actual dataset does have some fields with null values in it. but I filled in those with
., that is what I mean by there are no empty fields.
I am not sure what you mean by
already, you are correct that only
Classification is assigned a value.
The first condition does unconditionally set
Classification to
VUS. That seems to be working.
Condition 2 sets the
Classification to the value of
CLINSIG unless
CLINSIG has multiple values in it like in line 3 of
file (if there are multiple values in it they are separated by a
|. If this is the case then
Classification is
Conflicting.
Condition 3 is only run on the lines
where Func.IDP.refGene =
UTR then the value of
Classification is
Likely Benign,
if
CLINSIG is set to
VUS, if it is any other value it is not changed.
Condition 4 is if the
PopFreqMax >
.01 then the
Classification is
Likely Benign unless there is a value other
then
VUS there. If there is that means
CLINSIG had a value already.
Condition 5 is only run if
Func.IDP.refGene =
spicing AND
GeneDetail.IDP.refGene has
+/- symbol in it AND the number
after it is
> 10 then the value of Classification is Likely Benign, unless there is a value other
then
VUS there. If there is that means
CLINSIG had a value already.
Thank you
.