filtering_mutations: Filtering mutations with certain criteria

In itamuria/immunoeasy: Make Immuno Therapies An Easier Process

Filtering mutations with certain criteria

Description

Mutation list will be filtered based on some criteria

Usage

filtering_mutations(
  dataframe,
  variant_caller = "Mutect",
  PrimaryFilter = T,
  FuncRefGene = "exonic",
  ExonicFunc = "nonsynonymous_SNV",
  Cob_DNA_tum = 6,
  VAF_tum = 0.05,
  AD_alt_tum = 3,
  AD_alt = 1
)

Arguments

dataframe	The data frame with all the information
variant_caller	Select the variant caller that generated the data frame.
PrimaryFilter	If we want to apply PASS filter. Boolean with True by default.
FuncRefGene	What function of the Reference Gene we want to apply. Default is exonic.
ExonicFunc	What exonic function of the Reference Gene we want to apply. Default value is nonsynonymous_SNV
Cob_DNA_tum	Minimum deep of the tumoral DNA (bigger values will be considered).
VAF_tum	Minimum alternative frecuency of the tumor (bigger values will be considered).
AD_alt_tum	Minimum deep of alternative allele of the tumor (bigger values will be considered).
AD_alt	Maximum deep of alternative allele of the healthy tissue (smaller values and selected value will be considered).

Value

data frame filtered based on the selected criteria

Examples

## Not run: 
filtering_mutations (filename)

## End(Not run)

itamuria/immunoeasy documentation built on Sept. 30, 2022, 5:53 a.m.