visualizeGene {sesame} | R Documentation

## Visualize Gene

### Description

Visualize the beta value in heatmaps for a given gene. The function takes a gene name which is taken from the UCSC refGene. It searches all the transcripts for the given gene and optionally extend the span by certain number of base pairs. The function also takes a beta value matrix with sample names on the columns and probe names on the rows. The function can also work on different genome builds (default to hg38, can be hg19).

### Usage

    visualizeGene(
      geneName,
      betas,
      platform = c("EPIC", "HM450", "MM285"),
      upstream = 2000,
      dwstream = 2000,
      refversion = c("hg38", "hg19", "mm10"),
      ...
    )

### Arguments

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

### Value

None

### Examples

    betas <- sesameDataGet('HM450.76.TCGA.matched')$betas
    visualizeGene('ADA', betas, 'HM450')

[Package sesame version 1.12.9 Index]