limmaP {RnBeads} | R Documentation |
applies hierarchical modeling anlalogous to differential expression employed in the limma
package and returns
p-values for differential methylation
limmaP(X, inds.g1, inds.g2 = -inds.g1, adjustment.table = NULL, fun.conversion = rnb.beta2mval, paired = FALSE)
X |
Matrix on which the test is performed for every row |
inds.g1 |
column indices of group 1 members |
inds.g2 |
column indices of group 2 members |
adjustment.table |
a |
fun.conversion |
conversion function to transform the beta values into M values. By default, it is the logit function with adjustment
for infinity values. See |
paired |
should a paired analysis model be used. If so, the first index in |
vector of p-values resulting from limma's differential analysis
Requires limma
package
Fabian Mueller
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) meth.mat <- meth(rnb.set.example) sample.groups <- rnb.sample.groups(rnb.set.example)[[1]] p.vals <- limmaP(meth.mat,sample.groups[[1]],sample.groups[[2]])