dmpFinder | R Documentation |
Identify CpGs where methylation is associated with a continuous or categorical phenotype.
dmpFinder(dat, pheno, type = c("categorical", "continuous"),
qCutoff = 1, shrinkVar = FALSE)
dat |
A |
pheno |
The phenotype to be tested for association with methylation. |
type |
Is the phenotype '‘continuous’ or ‘categorical’? |
qCutoff |
DMPs with an FDR q-value greater than this will not be returned. |
shrinkVar |
Should variance shrinkage be used? See details. |
This function tests each genomic position for association between methylation and a phenotype. Continuous phenotypes are tested with linear regression, while an F-test is used for categorical phenotypes.
Variance shrinkage (shrinkVar=TRUE
) is recommended when sample
sizes are small (<10). The sample variances are squeezed
by computing empirical Bayes posterior means using the limma
package.
A table with one row per CpG.
Martin Aryee aryee@jhu.edu.
squeezeVar
and the limma package in general.
if (require(minfiData)) {
grp <- pData(MsetEx)$Sample_Group
MsetExSmall <- MsetEx[1:1e4,] # To speed up the example
M <- getM(MsetExSmall, type = "beta", betaThreshold = 0.001)
dmp <- dmpFinder(M, pheno=grp, type="categorical")
sum(dmp$qval < 0.05, na.rm=TRUE)
head(dmp)
}
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