binning: Methimpute binning functions

Description Usage Arguments Value Functions Examples

Description

This page provides an overview of all methimpute binning functions.

Usage

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binCounts(data, binsize)

binPositions(data, binsize)

binMethylome(data, binsize, contexts = "total", columns.average = NULL)

Arguments

data

A GRanges-class object with metadata columns 'context' and 'counts' (which is a matrix with columns 'methylated' and 'total').

binsize

The window size used for binning.

contexts

A character vector with contexts for which the binning will be done.

columns.average

A character vector with names of columns in data that should be averaged in bins.

Value

A GRanges-class object for binCounts and binPostions. A list() of GRanges-class objects for binMethylome.

Functions

Examples

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## Get some toy data
file <- system.file("data","arabidopsis_toydata.RData",
                    package="methimpute")
data <- get(load(file))
print(data)
## Bin the data in various ways
binCounts(data, binsize=1000)
binPositions(data, binsize=1000)
binMethylome(data, binsize=1000, contexts=c("total", "CG"),
            columns.average=NULL)

methimpute documentation built on Nov. 8, 2020, 5:47 p.m.