predictDIMPclass {MethylIT}R Documentation

Predict DIMP class


This function classify each DMP as a control or a treatment DMP


predictDIMPclass(LR, model, conf.matrix = FALSE, control.names = NULL,
  treatment.names = NULL)



A list of GRanges objects obtained through the through MethylIT downstream analysis. Basically, this object is a list of GRanges containing only differentially methylated position (DMPs). The metacolumn of each GRanges must contain the columna: Hellinger divergence "hdiv", total variation "TV", the probability of potential DMP "wprob", which naturally are added in the downstream analysis of MethylIT.


A classifier model obtained with the function 'evaluateDIMPclass'.


Optional. Logic, whether a confusion matrix should be returned (default, FALSE, see below).


Optional. Names/IDs of the control samples, which must be include in thr variable LR (default, NULL).


Optional. Names/IDs of the treatment samples, which must be include in the variable LR (default, NULL).


Predictions only makes sense if the query DMPs belong to same methylation context and derive from an experiment accomplished under the same condition set for the DMPs used to build the model.


The same LR object with tow new columns named "class" and "posterior" added to each GRanges object from LR (default). Based on the model prediction each DMP is labeled as control "CT" or as treatment "TT" in column "class". Column "posterior" provides, for each DMP, the posterior probability that the given DMP can be classified as induced by the 'treatment' (a treatment DMP).

Control DMPs classified as 'treatment' are false positives. However, if the same cytosine position is classified as 'treatment DMP' in both groups, control and treatment, but with higher posterior probability in the treatment group, then this would indicate a reinforcement of the methylation status in such a position induced by the treatment.

If "conf.matrix" is TRUE and the arguments control.names and treatment.names are provided, then the overall confusion matrix is returned.


data(cutpoint, PS, package = "MethylIT")

## DMPs are selected using the cupoints
DMPs <- selectDIMP(PS, div.col = 9L, cutpoint = cutpoint$cutpoint,
                   tv.cut = 0.92)

## Classification of DMPs into two clases: DMPS from control and DMPs from
## treatment samples and evaluation of the classifier performance (for more
## details see ?evaluateDIMPclass).
perf <- evaluateDIMPclass(LR = DMPs,
                          column = c(hdiv = TRUE, TV = TRUE,
                                     wprob = TRUE, pos = TRUE),
                          classifier = "lda", n.pc = 4L,
                          control.names =  c("C1", "C2", "C3"),
                          treatment.names = c("T1", "T2", "T3"),
                          center = TRUE, scale = TRUE,
                          prop = 0.6)

#' Now predictions of DMP for control and treament can be obtained
pred = predictDIMPclass(LR = DMPs, model = perf$model,
                        conf.matrix = TRUE,
                        control.names = c("C1", "C2", "C3"),
                        treatment.names = c("T1", "T2", "T3"))

[Package MethylIT version 0.3.1 ]