Compute the delta BIC for a list of potential models
Usage
DESeq2BIC(
data,
name = "BIC",
mode = "total",
normalization = mode,
formulas = list(Condition = ~Condition, Background = ~1),
no4sU = FALSE,
columns = NULL,
verbose = FALSE
)
Arguments
- data
A grandR object
- name
the user defined analysis name to store the results
- mode
either "total", "new" or "old"
- normalization
normalize on "total", "new", or "old" (see details)
- formulas
list of formulas specifying the models (you can use any column name from the
Coldata(data)
)- no4sU
Use no4sU columns (TRUE) or not (FALSE)
- columns
logical vector of which columns (samples or cells) to use (or NULL: use all)
- verbose
Print status updates
Value
a new grandR object including a new analysis table. The columns of the new analysis table are named as <name in list>.dBIC
Details
DESeq2 by default performs size factor normalization. When computing differential expression of new RNA, it might be sensible to normalize w.r.t. to total RNA, i.e. use the size factors computed from total RNA instead of computed from new RNA. This can be accomplished by setting mode to "new", and normalization to "total"!