pool-methods: Pool replicates within groups to a single sample per group

In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function sums up coverage, numCs and numTs values within each group so one representative sample for each group will be created in a new methylBase object

Usage

  pool(obj,sample.ids)

Arguments

obj	methylBase object with two groups or more and each group should have multiple samples
sample.ids	a character vector of new sample.ids ex:c("test","control"), should follow the same order as unique treatment vector, and should be equal to the length of the unique treatment vector

Value

a methylBase object

Author(s)

Altuna Akalin

Examples

library(methylKit)
data(methylKit)

# methylBase.obj has two groups, each group has two samples,
# the following function will pool the samples in each group
# so that each group will be represented by one pooled sample
pooled.methylBase=pool(methylBase.obj,sample.ids=c("test","control"))

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.