hummingbirdGraph {hummingbird}

R Documentation

Observations and Predictions Graphs

Description

This function generates observation and prediction graphs for a user specified region.

Usage

hummingbirdGraph(experimentInfoControl, experimentInfoCase, postAdjInfoDMRs,
                    coord1, coord2)

Arguments

experimentInfoControl	A SummarizedExperiment object containing the input data for the control group: The two assays: normM, normUM and the CpG position information: pos.
experimentInfoCase	A SummarizedExperiment object containing the input data for the case group: The two assays: abnormM, abnormUM and the CpG position information: pos.
postAdjInfoDMRs	The DMRs GenomicRanges object output of the hummingbirdPostAdjustment function.
coord1	The start coordinate of the genomic region to plot.
coord2	The end coordinate of the genomic region to plot.

Value

The function outputs two graphs: The Observations graph and the Predictions graph. The observation figure shows bin-wise average methylation rate for case and control groups. The prediction figure shows bin-wise prediction, where "0" denotes a predicted normal bin; "1" denotes a predicted hypermethylated bin; and "-1" denotes a predicted hypomethylated bin.

Examples

library(GenomicRanges)
library(SummarizedExperiment)
data(exampleHummingbird)
emInfo <- hummingbirdEM(experimentInfoControl = exampleSEControl,
                        experimentInfoCase = exampleSECase, binSize = 40)
postAdjInfo <- hummingbirdPostAdjustment(
                                    experimentInfoControl = exampleSEControl,
                                    experimentInfoCase = exampleSECase,
                                    emInfo = emInfo, minCpGs = 10,
                                    minLength = 100, maxGap = 300)
hummingbirdGraph(experimentInfoControl = exampleSEControl,
                    experimentInfoCase = exampleSECase,
                    postAdjInfoDMRs = postAdjInfo$DMRs,
                    coord1 = 107991, coord2 = 108350)

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