Fixes to various miscellaneous issues (#73, #84, #97, #122, #135, #142) #144
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…erlab#84: + check units and allow use of 'scaled_reads_per_base' + issue warning if user uses 'obs_raw' with an object in gene mode (since 'obs_raw' only contains transcript values)
…d) to address issue pachterlab#97
+ throws warning if in transcript mode + throws error if in gene mode to address issue pachterlab#122
+ This indirectly corrects issue pachterlab#135
… made API changes to data frame returned: + for LRT, the 'test_stat', 'rss', and 'degrees_free' columns are grouped after 'qval' to mimic the format of the Wald results table + if target mapping is included, the annotation columns come first
thanks to user @rakarnik for finding the missing space!
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Also added in improved error reporting when processing bootstraps using multiple cores. |
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Very nice. Thanks! |
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This pull request makes several small changes to address a few different issues:
sleuth_prepto make sure the full model does not result in singular matrix (issue Report a better error when design matrix is singular #73).sleuth_to_matrixwhen the object is in gene mode (issue sleuth_to_matrix reports transcripts even when an aggregation_column was provided to sleuth_prep #84)sleuth_gene_tableso that it now actually returns a data frame (issue Unstated namespace dependency on data.table::head #135)sleuth_resultsto include information about likelihood ratio test results (issue sleuth_results manpage does not document likelihood ratio result columns #142).get_kallisto_path.In addition to addressing these issues, I made a tweak to the API for the
sleuth_resultsso that it now returns the LRT columns in a group afterqval(similar to Wald results table columnsbandse_b), and if there are any target mapping columns, those annotation columns are shown before any of the other result columns.