filterMutations: filterMutations: remove or keep specified mutations

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

filterMutations: remove or keep specified mutations

Description

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

Usage

filterMutations(object 
, filtered=NULL 
, bed = NULL 
, mode = c("exclude" , "keep") 
, tumor_type=NULL)

Arguments

object	An instance of class CancerPanel
filtered	A data.frame used as filter
bed	A data.frame in bed format (chr start end)
mode	If "exclude", mutations are removed from the object. If "keep", mutations specified in filtered are the only ones maintained.
tumor_type	A vector of tumor_type names. The filter will be active only on the specified tumor types

Details

filtered data.frame can come in three different formats:

1. "gene_symbol" , "amino_position" Ex. BRAF 600

2. "gene_symbol" , "amino_acid_change" Ex. BRAF V600E

3. "genomic_poistion" Ex. 3:1234567:A,C

bed file must be composed by 3 columns: chrN, start 0-base , end 1-base

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 filterFusions

Examples

# Retrieve example data
data(cpObj)
# Create a data.frame to filter
myFilter <- data.frame(gene_symbol = c("BRAF" , "PIK3CA") 
    , amino_position = c(600 , 118))
# Keep only myFilter mutations
cpObjKeep <- filterMutations(cpObj , filtered = myFilter , mode = "keep")
# Exclude myFilter mutations
cpObjExclude <- filterMutations(cpObj , filtered = myFilter , mode = "exclude")

# Create a bed file
myBed <- data.frame(chr = paste0("chr" , c(7 , 17)) 
    , start = c(140534632 , 41244326) 
    , end = c(140534732 , 41244426) , stringsAsFactors=FALSE)
# Keep only myFilter mutations
cpObjKeep <- filterMutations(cpObj , bed = myBed , mode = "keep")
# Exclude myBed mutations
cpObjExclude <- filterMutations(cpObj , bed = myBed , mode = "exclude")

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