Comments (3)
torognes
commented on September 25, 2024
CompAIRR cannot directly compute metrics like Jaccard or Morisita-Horn index, so that has to be done afterwards.
It will only compute the sum of the products of the counts of all the matching sequences. Please see the overlap example in the README for details. Instead of the sum of the products of the counts, it can also compute the sum of the ratio, min, max, or mean, as indicated by the -s option. This may be helpful with some metrics.
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torognes
commented on September 25, 2024
We could consider adding this as a feature in the future.
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torognes
commented on September 25, 2024
Computation of the Morisita-Horn or Jaccard index have been added in version 1.7.0. Use the option -s MH or -s Jaccard, respectively.
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Related Issues (20)
- Timestamps at major steps in the analysis HOT 1
- Option to selected alternative ways to compute output values HOT 3
- Max 65535 repertoires HOT 1
- Option to compare a set of sequences against a repertoire HOT 3
- Handle non-standard sequence symbols better HOT 2
- Segmentation fault when clustering sequences HOT 5
- Is sequence matching exact? HOT 3
- Segfault with very short sequences with d=3 HOT 1
- Allow d>3 HOT 1
- Unable to upgrade version HOT 3
- compairr MH index strange results HOT 10
- Detect duplicates in the input HOT 2
- Compute table of hamming distances between all sequences HOT 1
- Extracting information on the distance HOT 2
- Increase resolution of timing of operations HOT 2
- New feature: Copy additional columns from input to output files HOT 2
- Default repertoire ID if column missing HOT 1
- A flag to switch to cdr3 instead of junction HOT 1
- Allow multiple indels or more substitutions with a single indel HOT 1
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