visualizeProbes {sesame} | R Documentation

## Visualize Region that Contains the Specified Probes

### Description

Visualize the beta value in heatmaps for the genomic region containing specified probes. The function works only if specified probes can be spanned by a single genomic region. The region can cover more probes than specified. Hence the plotting heatmap may encompass more probes. The function takes as input a string vector of probe IDs (cg/ch/rs-numbers). if draw is FALSE, the function returns the subset beta value matrix otherwise it returns the grid graphics object.

### Usage

    visualizeProbes(
      probeNames,
      betas,
      platform = c("EPIC", "HM450", "MM285"),
      refversion = c("hg38", "hg19", "mm10"),
      upstream = 1000,
      dwstream = 1000,
      ...
    )

### Arguments

`probeNames` | probe names
`betas` | beta value matrix (row: probes, column: samples)
`platform` | HM450, EPIC or MM285 (default)
`refversion` | hg19, hg38 or mm10 (default)
`upstream` | distance to extend upstream
`dwstream` | distance to extend downstream
`...` | additional options, see visualizeRegion

### Value

None

### Examples

    betas <- sesameDataGet('HM450.76.TCGA.matched')$betas
    visualizeProbes(c('cg22316575', 'cg16084772', 'cg20622019'), betas, 'HM450')

[Package sesame version 1.12.9 Index]