Description Usage Arguments Value Functions Note Examples
A convenience wrapper for limma
1 2 3 |
eset |
eset (or most likely eset subclass) object |
model.str |
character formulation of the model (e.g. "~ a + b") |
coef.str |
character coefficient of interest. E.g. "a". Either numeric or factor with 2 levels. |
... |
arguments for |
data.frame. Basically output of
topTable
function.
limma_gen
: More generalized approach. The tested variable doesn't have to be a
factor with 2 levels like in limma_a_b.
limma_a_b is for either 2-factor ANOVA or linear regression.
limma_gen is a more generic version and will return results
for all the coefficients that match coef.str
pattern.
1 2 3 4 5 6 7 8 9 10 11 12 | library("vp.misc")
data("cptac_oca")
library("limma")
ee <- oca.set
ee <- ee[rowSums(!is.na(exprs(ee))) >= 30,]
model.string <- "~ PLATINUM.STATUS + AGE" # model with covariates
coef.string <- "PLATINUM.STATUS" # note, only two levels allowed here
res <- limma_a_b(oca.set,
model.str = "~ PLATINUM.STATUS + AGE",
coef.str = "PLATINUM.STATUS")
head(res)
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