Description Usage Arguments Value Author(s) Examples
View source: R/plmDEmodel.default.R
Given gene expression data as well as phenotypic measurements, plmDEmodel
encodes them within a single object on which fitGAPLM
and limmaPLM
can be run.
1 2 | ## Default S3 method:
plmDEmodel(genes, expressionValues, sampleInfo, ...)
|
genes |
A vector of the genes (or probes/targets) from which each one is to be tested for differential expression. |
expressionValues |
A data frame or matrix containing the expression data of these genes. Each column should represent one sample and each row one gene. |
sampleInfo |
Information about the samples in |
... |
Parameters from |
Returns an object of type plmDE
on which fitGAPLM
may be run to test for differential expression under a specified model.
Jonas Mueller
1 2 3 4 5 6 7 8 9 | ## create an object of type \code{plmDE} containing disease
## with "control" and "disease" and measurements of weight and severity:
ExpressionData = as.data.frame(matrix(abs(rnorm(10000, 1, 1.5)), ncol = 100))
names(ExpressionData) = sapply(1:100, function(x) paste("Sample", x))
Genes = sapply(1:100, function(x) paste("Gene", x))
DataInfo = data.frame(sample = names(ExpressionData), group = c(rep("Control", 50),
rep("Diseased", 50)), weight = abs(rnorm(100, 50, 20)), severity = c(rep(0, 50),
abs(rnorm(50, 100, 20))))
plmDEobject = plmDEmodel(Genes, ExpressionData, DataInfo)
|
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