Description Usage Arguments Value Examples
This function allows to perform an association study between gene
expression from microarray and the exposome. An ExpresionSet
is
the object storing the gene expresion and an ExposomeSet
the one
storing the exposome. Both of them needs to be encapsulated in a
MultiDataSet
. The association study is perform through standard
limma
pipeline. The function allows to perform multiple tests using
the argument exposures
.
1 2 3 4 5 6 7 8 | association(object, formula, expset, omicset, set = "exposures",
method = "ls", ..., baselevels, sva = "none", vfilter = NULL,
verbose = FALSE, warnings = TRUE)
## S4 method for signature 'MultiDataSet'
association(object, formula, expset, omicset,
set = "exposures", method = "ls", ..., baselevels, sva = "none",
vfilter = NULL, verbose = FALSE, warnings = TRUE)
|
object |
A |
formula |
formula to be evaluated by each exposure (or phenotype, see
|
expset |
Name of the |
omicset |
Name of the omic data-set in |
set |
(default |
method |
(default |
... |
Arguments passed to |
baselevels |
(optional) If set, must be a labeled vector with the default base level for categorical exposures. |
sva |
(default |
vfilter |
(default |
verbose |
(default |
warnings |
(default |
An object of class ResultSet
.
1 2 3 4 5 6 7 8 9 10 | library(MultiDataSet)
data(brge_prot, package = "brgedata")
data(brge_expo, package = "brgedata")
mds <- createMultiDataSet()
mds <- add_eset(mds, brge_prot, dataset.type = "proteines")
mds <- add_eset(mds, brge_expo, dataset.type = "exposures", GRanges = NA)
asr <- association(mds, formula = Asthma ~ Sex + Age,
expset = "exposures", omicset = "proteines")
asr
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.