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erhard-lab / grandR

R package for nucleotide conversion sequencing data analysis
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classify.genes does not work as intended #5

Closed Lygeri-Sakellaridi closed 2 years ago

Lygeri-Sakellaridi commented 2 years ago

It creates the user-specified gene types, but does not assign any genes to them even when appropriately named genes exist in the object.

See loading-data vignette, lines 223-249

florianerhard commented 2 years ago

It actually works as intended, its documentation was just really, really bad: It's now:

The classify.gene} list can be used to define gene types. Each element must be a function that returns either a logical or numeric vector that identifies genes (i.e. all entries that are TRUE, or numbers used as indices). The type of all identified genes then is the name of the list entry. If a gene receives multiple types, the first in the list is used!

Please change this in the vignette!