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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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Helping local execution of code producing figures #118

Closed smoe closed 2 years ago

smoe commented 2 years ago

~The introduced "require(DESeq2)" would solve the error message i ran into about the unknown method "counts" that was referenced. I then saw a few lines below that you indicated the the same routine by its full name DESeq2::counts and adopted that also for the first invocation, so "require" to my understanding is no longer needed (I still like it, though).~

smoe commented 2 years ago

Ok. I finally found in scripts/deseqReport.Rmd.in in line 45 the hidden block providing the setup. This explains why I ran into this. I'll then continue adding the "require" where the respective package is used. WIth the additional argument "quietly=T" I do not expect too much harm to shift this down to the visible parts.

smoe commented 2 years ago

The 'quietly=TRUE' for require() is in parts completely ignored when the package is first loaded. But subsequent loads are fine, it should hence be fine to add the required lines since they should not interfere with the output.

The assignments of the functions melt and SharedData to reshape2 and crosstalk I suggest to help with the package prefixes.

Please have another look at the line the conditionally sets the header for the GO terms. Here you want to set the echo=FALSE.