Helping you to draft the materials and methods section
Usage
matmetmaker_RNAseqbulk(
dds_object,
template_text = NULL,
packages = NULL,
FDRthreshold = NULL,
de_framework = "DESeq2",
add_citations = TRUE
)Arguments
- dds_object
A
DESeqDatasetobject. Necessary to read in the info on how the quantifications were performed. Thankstximeta!- template_text
A (long, correctly structured) character string. It defaults to NULL, which would then lead to using the "default" content. TODO: To implement and possibly use "custom"/personalized ones, that could ideally live in separated files (one for each? one for type?)
- packages
Character vector. Defaults to NULL. Specifies which packages would need to be captured, alongside the "standard" ones.
- FDRthreshold
Numeric value, specifying a precise FDR value. If left unspecified (NULL by default) it searches for the value in the environment of the variable called
FDR.- de_framework
Character string, defaults to "DESeq2"- if implemented in other frameworks we could use this to swap some behavior.
- add_citations
Logical value, TODO to be implemented. In its implementation it should add after the tools the relevant DOIs and/or PMIDs to the articles it should refer to. This should simplify our lives and the lives of our collaborators to add the relevant references into the manuscripts.