filterFusions {PrecisionTrialDrawer} | R Documentation

## filterFusions: remove or keep specified fusions

### Description

This method allows to keep only or to exclude certain fusions according to three different filtering formats

### Usage

    filterFusions(object , filtered , mode = c("exclude" , "keep"))

### Arguments

`object` | An instance of class CancerPanel
`filtered` | A character vector used as filter
`mode` | If "exclude", fusions are removed from the object. If "keep", fusions specified in filtered are the only ones maintained.

### Details

filtered vector must be in fusion format GENE1\_\_GENE2.

At the end of the filtering procedure, subsetAlterations is automatically run.

### Value

An updated instance of class CancerPanel

### Author(s)

Giorgio Melloni , Alessandro Guida

### References

data origin for mutations , copynumber and expression data

data origin for fusion data

### See Also

`getAlterations` `subsetAlterations` `filterMutations`

### Examples

    # Retrieve example data
    data(cpObj)
    # Create a data.frame to filter
    myFilter <- c("ERC1__RET", "TRIM33__RET", "EML4__ALK")
    # Keep only myFilter fusions
    cpObjKeep <- filterFusions(cpObj , filtered = myFilter , mode = "keep")
    # Exclude myFilter fusions
    cpObjExclude <- filterFusions(cpObj , filtered = myFilter , mode = "exclude")

[Package PrecisionTrialDrawer version 1.4.0 Index]