mennodejong1986
commented
1 year ago Thanks for the feedback! Indeed, this was confusing or in fact incorrect.
The statement has now been clarified to: "Pairwise_relatedness.txt file is not present or does not have the expected number of rows, or flag do_overwrite (flag 'overwrite_kindf' of wrapper calckinship function)is set to TRUE (default setting)."
The reason that the dataframe is by default recreated is to avoid errors which may arise when the filter settings have been changed.
Hi, This isn't a big issue but it does lead to a lot of time being "wasted" by the users of your excellent software!
When I run calckinship() this is always printed out during the analysis: "Pairwise_relatedness.txt file is not present or does not have the expected number of rows, or flag do_overwrite is set to TRUE. Creating datafile now. This will take some time, but the next time you run the calckin() function this step will be automatically omitted and then it will be much faster."
I thought that do_overwrite must be set to FALSE as the DEFAULT based on the way this statement reads, but it turns out apparently it is not. I should have realized that sooner - but it has taken me several goes with running this function to finally get that I need to change from the default to stop rerunning this time consuming step. Part of the problem is that I actually look at your manual (very helpful) and there is no function argument "do_overwrite" choice in the calckinship() section.
Just thought it might be helpful to others to be aware of this issue. Best,