filterFusions: filterFusions: remove or keep specified fusions
In PrecisionTrialDrawer: A Tool to Analyze and Design NGS Based Custom Gene Panels

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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.

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

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

An updated instance of class CancerPanel

Giorgio Melloni , Alessandro Guida

data origin for mutations , copynumber and expression data

data origin for fusion data

getAlterations subsetAlterations filterMutations

# 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")