comparative_expression_2017's Issues
Species NA
Cat noted that there are some NA
s for species in expression
after:
left_join( tip_annotations, by="Ensembl.Gene.ID" )
in https://github.com/caseywdunn/comparative_expression_2017/blob/master/manuscript.rmd
This could be due to errors in parsing tip_annotations
or due to missing data in the SEQ fields.
change execution model
At present all the analyses are in manuscript.rmd
. This is getting cumbersome to work with as most of the code is stable but increasingly computationally expensive.
Switch to a model where:
-
All computationally intensive analyses are run by
manuscript_kernel.R
. This can be generated by modifiedknit::purl()
output. -
manuscript_kernel.R
saves amanuscript.RData
file. It has no other output or side effects. This file is not checked into the repo, as it is anticipated to be >250MB in size. It can be moved between computers (eg executed on the cluster and then moved to laptop). The docker code will facilitate consistent environment. -
manuscript_kernel.R
can also save intermediatemanuscript_checkpoint_XX.RData
files to facilitate debugging when the code does not run to completion. -
All code in
manuscript_kernel.R
will be removed frommanuscript.rmd
.manuscript.RData
will be loaded withload()
. The manuscript will contain inline code, plot rendering, and very lightweight analyses.
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