Update write_kallisto_hdf5 function and add ability to subset kallisto object (address #131)
#150
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+ add a sanity check to make sure that the target_ids given are actually a character vector + add 'excluded_ids' and 'original_num_targets' to kallisto object to keep track of how a kallisto object has been subsetted + add functions to report subset status and any excluded IDs + modify print function for kallisto to include subset status
…h Wald from LRT results; this is to finish work on addressing issue pachterlab#142
…sto files and in the target mapping
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The last commit is relating to this discussion on the forum: potential bug in sleuth_prep related to class of target_id |
+ This fixes issue pachterlab#151 + Thanks to @petersbr for the suggested edit
warrenmcg
changed the title
write_kallisto_hdf5 function and add ability ot subset kallisto object (address #131)write_kallisto_hdf5 function and add ability to subset kallisto object (address #131)
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Hi @pimentel,
Thanks to the work of @agropyron and small tweaks, we have a working write function. I've added some S3 methods (with updated documentation and
NAMESPACE) to subsetkallistoobjects (or the collection ofkallistoobjects within a sleuth object). This should address issue #131.When I did a checkout of the recent commit on the
develbranch, there were several miscellaneous things related to the documentation andNAMESPACEforgene_for_genethat need to be fixed, so I'll be including those here too.Only issue right now is that if a user subsets kallisto objects within a sleuth object, there isn't a way for the user to know to rerun
sleuth_prep, and there will now be mismatch between theobj$kaland the rest of the object. There isn't an easy way to rerunsleuth_prepwith just theobj$kallist, so should we implement that?