Gdr 2682 #132
Gdr 2682 #132
Conversation
darsoo
requested review from
j-smola and
bczech
and removed request for
a team
|
Please reoxygenate the documentation |
|
@darsoo Please reoxygenate the documentation |
| duplicated_ids <- setdiff(duplicated_ids, duplicated_ids_with_clid) | ||
| } else { | ||
| duplicated_ids <- col_data[[cellline_name]][duplicated(col_data[[cellline_name]])] | ||
| } |
There was a problem hiding this comment.
Why there is a different procedure for colData for SE and for data.table?
(I understand that in colData we do not have information about Drug, but it is misleading: the same content as input but different output depending on format - in the context of presence of cell line name duplicates)
> dt <- data.table::data.table(
DrugName = c("DrugA", "DrugB", "DrugC", "DrugD", "DrugC", "DrugD"),
Gnumber = c("G1", "G2", "G3", "G4", "G3", "G4"),
CellLineName = c("ID1", "ID1", "ID2", "ID2", "ID2", "ID2"),
clid = c("C1", "C2", "C3", "C4", "C5", "C6")
)
> res_dt <- set_unique_cl_names_dt(dt)
> res_dt
DrugName Gnumber CellLineName clid
<char> <char> <char> <char>
1: DrugA G1 ID1 C1
2: DrugB G2 ID1 C2
3: DrugC G3 ID2 (C3) C3
4: DrugD G4 ID2 (C4) C4
5: DrugC G3 ID2 (C5) C5
6: DrugD G4 ID2 (C6) C6
dt <- S4Vectors::DataFrame(
DrugName = c("DrugA", "DrugB", "DrugC", "DrugD", "DrugC", "DrugD"),
Gnumber = c("G1", "G2", "G3", "G4", "G3", "G4"),
CellLineName = c("ID1", "ID1", "ID2", "ID2", "ID2", "ID2"),
clid = c("C1", "C2", "C3", "C4", "C5", "C6")
)
> res_S4 <- set_unique_cl_names_dt(dt)
> res_S4
DataFrame with 6 rows and 4 columns
DrugName Gnumber CellLineName clid
<character> <character> <character> <character>
1 DrugA G1 ID1 (C1) C1
2 DrugB G2 ID1 (C2) C2
3 DrugC G3 ID2 (C3) C3
4 DrugD G4 ID2 (C4) C4
5 DrugC G3 ID2 (C5) C5
6 DrugD G4 ID2 (C6) C6
There was a problem hiding this comment.
I see your point, but in my opinion it's a bit pointless. From a practical point of view DataFrame is only used for colData or rowData in SE, where there is no possibility for such a situation to occur. I don't see the need to complicate this logic.
More complex logic for data.table objects is required due to data specificity.
There was a problem hiding this comment.
IMO now is complicated and not consistent.
I would vote for the function always returning the same result, regardless of format. The user may want to use this feature in a context other than within the application.
The only thing to change is - instead of checking format of col_data input - just check whether unique_col_names is "CellLineName".
If true - just add suffix, if not - check other columns and add suffix accordingly.
You have that code already written.
There was a problem hiding this comment.
Yes but duplicated works in different way for data.table and DataFrame.
There was a problem hiding this comment.
I'm on the same page as @j-smola. It would be great to have consistent logic regardless of the data format.
There was a problem hiding this comment.
Ok. Added fix and test
Co-authored-by: j-smola <[email protected]>
|
Please, reoxygenate the documentation (run |
done |
Description
What changed?
Related JIRA issue:
Why was it changed?
Checklist for sustainable code base
Logistic checklist
Screenshots (optional)