lgatto/synapter — pull request #61 by sgibb (2014-04-30 10:01:07+00:00)
Title: add argument ILequal to dbUniquePeptideSet; closes #60

Dear Laurent,

this PR adds the argument `ILequal` to `dbUniquePeptideSet`. If `TRUE` (default) *I* and *L* are treated as identical and `"ABCL"` and `"ABCI"` are removed. If `FALSE` there are kept as unique.

Questions:
1. `ILequal` is a stupid name. Do you have a better suggestion for the name of the argument?
2. I am not convinced that this should be the default behaviour. Should we set `ILequal = TRUE` or `ILequal = FALSE` as default?

Best wishes,

Sebastian

/cc @pavel-shliaha