filterFusions: filterFusions: remove or keep specified fusions

In gmelloni/PrecisionTrialDesigner: A Tool to Analyze and Design NGS Based Custom Gene Panels

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")

gmelloni/PrecisionTrialDesigner documentation built on March 3, 2023, 6:10 a.m.