Skip to content

Feature consideration: Change the default "group" header to reflect what the group column represents #10

Description

@jlanej

When writing output files, we default to having a column named "group" in the header

https://github.com/PankratzLab/kd-match/blob/435d6d159e399723974071eaddfe3cdb0792cf9d/src/main/java/org/pankratzlab/kdmatch/KDMatch.java#L114 .

The group column corresponds to a category that must be matched within … so if cases and controls had to be the same sex, the group would either be male/female or 1/2 etc. If they had to be the same sex, from the same sequencing center, and ancestry, the groups would be appended and would look like 2_UMGC_AFR or 1_UMGC_AFR. In this example, we could consider changing the group header to instead be something like "Group_Matched_within_Sex_SequencingCenter_Ancestry" (or whatever the corresponding input files contained in the header). But after writing that out, it starts to look like a very long header... so maybe it isn't the best way forward.

The updated header would potentially be passed to the methods writing the output files here

KDMatch.writeToFile(naiveMatches.stream(), outputBaseFileName,
setConvert.stream().toArray(String[]::new),
setConvert.stream().toArray(String[]::new), initialNumSelect);
or here
KDMatch.writeToFile(optimizedMatches.stream(), outputOptFileName,
setConvert.stream().toArray(String[]::new),
setConvert.stream().toArray(String[]::new), finalNumSelect);

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions