cnvOncoPrint {CNVRanger} | R Documentation

## OncoPrint plot for CNV regions

### Description

Illustrates overlaps between CNV calls and genomic features across a sample population.

### Usage

    cnvOncoPrint(
      calls,
      features,
      multi.calls = .largest,
      top.features = 25,
      top.samples = 100,
      ...
    )

### Arguments

`calls` | Either a `GRangesList` or `RaggedExperiment` storing the individual CNV calls for each sample.
`features` | A `GRanges` object containing the genomic features of interest, typically genes. Feature names are either expected as a meta-column `symbol` or as the `names` of the object.
`multi.calls` | A function. Determines how to summarize the CN state in a CNV region when there are multiple (potentially conflicting) calls for one sample in that region. Defaults to `.largest`, which assigns the CN state of the call that covers the largest part of the CNV region tested. A user-defined function that is passed on to `qreduceAssay` can also be provided for customized behavior.
`top.features` | integer. Restricts the number of features for plotting to features experiencing highest alteration frequency. Defaults to 25. Use `-1` to display all features.
`top.samples` | integer. Restricts the number of samples for plotting to samples experiencing highest alteration frequency. Defaults to 100. Use `-1` to display all samples.
`...` | Additional arguments passed on to `ComplexHeatmap::oncoPrint`

### Value

None. Plots to a graphics device.

### Author(s)

Ludwig Geistlinger

### See Also

`ComplexHeatmap::oncoPrint`

### Examples

    # read in example CNV calls
    data.dir <- system.file("extdata", package="CNVRanger")
    call.file <- file.path(data.dir, "Silva16_PONE_CNV_calls.csv")
    calls <- read.csv(call.file, as.is=TRUE)

    # store in a GRangesList
    calls <- makeGRangesListFromDataFrame(calls,
       split.field="NE_id", keep.extra.columns=TRUE)

    # three example genes
    genes <- c(  "chr1:140368053-140522639:-",
                 "chr2:97843887-97988140:+",
                 "chr2:135418586-135422028:-")
    names(genes) <- c("ATP2C1", "MAP2", "ACTL8")
    genes <- GRanges(genes)

    # plot
    cnvOncoPrint(calls, genes, top.samples = 25)

[Package CNVRanger version 1.4.3 Index]