Harmonize (merge) helper functions from the different pipelines
Merge (+parametrize when necessary) redundant helper functions from the different pipelines.
The functions will live in the R
folder of the package.
I suggest to keep them in separate files:
-
common.R
has functions that can be called from all reports (eg.ChIPhelper.Bowtie()
-->common.Bowtie()
or justbowtie()
) -
ChIP.shinyrep.helpers.R
functions specific to the ChIPseq report (eg.ChIPhelper.IPstrength()
) - same for the other reports
-
misc.R
private functions that do random things, like creating a color palette. It's not strictly necessary, but will help to keep the other files less messy.
Currently I copied all the helper functions from the different reports into the R
folder. But didn't do any work yet and probably the package wouldn't even build with all those library()
calls in the head of the Rmd files.