get.methylDiff-methods: get differentially methylated regions/bases based on cutoffs

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function subsets a methylDiff object in order to get differentially methylated bases/regions satisfying thresholds.

Usage

  get.methylDiff(.Object,difference=25,qvalue=0.01,type="all")

Arguments

.Object	a methylDiff object
difference	cutoff for absolute value of methylation change between test and control (default:25)
qvalue	cutoff for qvalue of differential methylation statistic (default:0.01)
type	one of the "hyper","hypo" or "all" strings. Specifies what type of differentially menthylated bases/regions should be returned. For retrieving Hyper-methylated regions/bases type="hyper", for hypo-methylated type="hypo" (default:"all")

Value

a methylDiff object containing the differential methylated locations satisfying the criteria

Examples

data(methylKit)

# get differentially methylated bases/regions with specific cutoffs
all.diff=get.methylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="all")

# get hyper-methylated
hyper=get.methylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hyper")

# get hypo-methylated
hypo=get.methylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hypo")

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.