-
Notifications
You must be signed in to change notification settings - Fork 0
Description
When writing output files, we default to having a column named "group" in the header
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); |
MatchSamples/src/main/java/org/pankratzlab/internal/gwas/MatchMaker.java
Lines 99 to 101 in 43a5338
| KDMatch.writeToFile(optimizedMatches.stream(), outputOptFileName, | |
| setConvert.stream().toArray(String[]::new), | |
| setConvert.stream().toArray(String[]::new), finalNumSelect); |