scoreAnnotatedDMRs: Score the annotated methylation segments.

In GianlucaMattei/methyl.O: Annotate, Score and Visualize Differentially Methylated Regions

Score the annotated methylation segments.

Description

Assigns a score to annotated methylated segments resulting from annotateDMRs() function

Usage

scoreAnnotatedDMRs(
  annotatedDMRs,
  active.features = c("promoters", "heads"),
  score.modifier = 0.5
)

Arguments

annotatedDMRs	anotated DMRs list resultingfrom annotateDMRs()
active.features	character vectors, containing features to correlate. Must be from names of resulting list from annotateDMRs. Additional feature names can be first exons (exons1) or first intron (intron1). To use more than one feature use c(). Default = c("promoters", "heads")
score.modifier	numeric, value between 0-1. It specifies how the final score is computed by assigning different weights to the methylation charactersistics of enhacners or to genes already involved in pathologies. By increasing this value to 1, resulting scores will be focused on discovering segments affecting gene expression. A value equal to 0 will focus the results on enahcners involving genes associated to pathologies, not considering the effect of methylation. Default = 0.5

Value

data.frame of annotated DMRs with assigned scores

GianlucaMattei/methyl.O documentation built on Sept. 12, 2023, 11:53 p.m.