selkamand / sigstash

Easily load published mutational signatures into R
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easier creation of custom signature datasets #20

Closed selkamand closed 5 months ago

selkamand commented 5 months ago

sigstash should allow the user to easily create custom signature sets by combining different signatures from various collections.

While the user can obviously already do this by subsetting and combining the sigstash collections (since they're just named lists) - we can make it easier by offering the following functions

1.sig_subset(collection, signatures) which takes a signature collection and selects a subset (returns a signature collection).

  1. sig_merge(...) which takes n signature collections and adds them together (checking for duplicate signature names)
  2. sig_convert(collection, format = c("sigminer", "tidy")) which converts a sigstash style collection to sigminer or tidy formats
selkamand commented 5 months ago

Unfortunately the classless nature of sigverse means we can't automatically bring the sigstash annotations along with the signatures.

If we need to, down the line we could add sig_subset_annotations(annotations, signatures) and sig_merge_annotations(annotations1, annotations2)

selkamand commented 5 months ago

We ended up not adding sig_convert, since we already have sig_collection_to_sigminer()

We should probably add a sig_collection_to_tidy() then rework sig_load to use these .. but that should be a separate issue