This is branched from include_r_pkg branch, thus contains all the commits from that branch too. In include_r_pkg, an R package (R.ODAF.utils) was made to house our many R functions in a more manageable way. Some notes from that:
params may be altered a bit. Will note here and update when I have to change something so we can go back and cross reference schemas and configs and Rmd files.
using a single function for get_params simplifies things, but also might mean that a few parameters belong more in the 'common' section, which means that change will need to be propagated.
solvent_control is an example
Otherwise: I'm planning to use function arguments (e.g., context = "analysis" vs "QC") to have control structures that specify how a function should run in the context of the QC script vs DESeq/report generation
This branch incorporates the R package as part of the R-ODAF_Health_Canada repo rather than installing it into the environment from a separate repo.
Note that a few of the checksums do not match the truth_checksums used during the github workflow, but they are consistent with what I get locally. This is very likely due to rounding differences. But it means the tests won't pass until changed.
mattjmeier
commented
2 months ago
This is branched from include_r_pkg branch, thus contains all the commits from that branch too. In include_r_pkg, an R package (R.ODAF.utils) was made to house our many R functions in a more manageable way. Some notes from that:
params may be altered a bit. Will note here and update when I have to change something so we can go back and cross reference schemas and configs and Rmd files. using a single function for get_params simplifies things, but also might mean that a few parameters belong more in the 'common' section, which means that change will need to be propagated. solvent_control is an example Otherwise: I'm planning to use function arguments (e.g., context = "analysis" vs "QC") to have control structures that specify how a function should run in the context of the QC script vs DESeq/report generation
This branch incorporates the R package as part of the R-ODAF_Health_Canada repo rather than installing it into the environment from a separate repo.
Note that a few of the checksums do not match the truth_checksums used during the github workflow, but they are consistent with what I get locally. This is very likely due to rounding differences. But it means the tests won't pass until changed.