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)

[Package hummingbird version 1.4.0 Index]