plot.cher {Ringo} | R Documentation

## Plot identified Chers

### Description

Function for plotting identified Chers (ChIP-enriched regions).

### Usage

    ## S4 method for signature 'cher,ExpressionSet'
    plot(x, y, probeAnno, samples=NULL, extent = 1000, gff = NULL, ...)

### Arguments

`x` | object of class `cher`
`y` | data object of class `ExpressionSet` that was used for function `findChersOnSmoothed`
`probeAnno` | object of class `probeAnno` holding the reporter/probe to genome mappings
`samples` | which samples to plot, either a numeric vector of entries in 1 to `ncol(dat)`, or character vector with entries in `sampleNames(dat)` or `NULL` meaning plot the levels from all samples in the ExpressionSet
`extent` | integer; how many base pairs to the left and right should the plotted genomic region be extended
`gff` | data frame with gene/transcript annotation
`...` | further arguments passed on to function `chipAlongChrom`

### Value

called for generating the plot; `invisible(NULL)`

### Author(s)

Joern Toedling

### See Also

`chipAlongChrom`, `cher-class`

[Package Ringo version 1.56.0 Index]