Patch: bugs in sleuth_results & other miscellaneous fixes #163
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warrenmcg
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warrenmcg
changed the title
…on in sleuth_results
+ this is in case it is a data.table or other extended data frame object + this addresses issue pachterlab#153
warrenmcg
changed the title
+ also added a warning if metadata for the gene-level analyses results in multiple entries for any genes.
+ show_all before pval_aggregate broke the lancaster function, so it's now after + show_all and combining metadata works the same for both pval_aggregate and gene_mode, but only if pval_aggregate maintains that the first column is called "target_id"
+ read_kallisto now always records the number of bootstraps present and the number that will be used for analysis, regardless of whether it actually reads those bootstraps + the number of bootstraps found and used are now stored as attributes for the kallisto object + the summary function for sleuth objects will now print both the number of bootstraps found and the number used for analysis
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Looks great -- as usual, thanks, @warrenmcg! |
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Hi @pimentel,
sleuth_resultsbugs:I discovered two bugs in
sleuth_results:show_all = Fstill results in all target_ids being returned.pvalue_aggregate = Tresults in the extra annotation data being missing.I made the following changes to the function to hopefully correct this behavior.
spread_abundance_byspeed-upI also earlier had made a faster version of
spread_abundance_by, and realized that it make it in the propagation forward of merged changes. That version is found below, and I have confirmed that it produces identical results in at least three separate datasets with differenttarget_ids. Yet, it has a 3-fold increase in speed. It's a small gain overall, but it greatly affects thesleuth_liveexperience since plotting functions heavily usespread_abundance_by, and it affects to a small extent sleuth-ALR overall speed.NAMESPACE issue with
transform_statusWhen running
devtools::document(), the NAMESPACE updatedtransform_statusfrom a regular method to an S3method.sample_to_covariates
data.tableerror, addressing issue #153When a
sample_to_covariatestable is provided tosleuth_prepas adata.tableobject, it passes thedata framecheck in place, but causes downstream problems. I put in a line to coerce any table that passes the check to adata frame.Best,
Warren