filter_mut_table: Filter raw mutation tables

In xmc811/xmcutil: Bioinformatics data processing utilities

Description

Filter raw mutation tables

Usage

filter_mut_table(
  table,
  t_cov = 15,
  n_cov = 8,
  t_frac = 0.02,
  n_frac = 0.01,
  pop_freq = 0.01
)

Arguments

table	A dataframe - the mutation table downloaded from server
t_cov	An integer - the minimum coverage for tumor sample
n_cov	An integer - the minimum coverage for normal sample
t_frac	A double - the minimum allele fraction in tumor sample
n_frac	A double - the maximum allele fraction in normal sample
pop_freq	A double - the maximum population frequncy

Value

A dataframe - the table with added columns

xmc811/xmcutil documentation built on June 4, 2021, 10:48 a.m.