create_final_filtered_dataframe: Create the final filtered dataframe.

In shlienlab/ShlienLab.Core.SSM: Simple Somatic Mutation (SSM) library.

Description

Creates the hard filtered final dataframe by removing PON, cFilter, soft clipped and hard clipped filtered data from the input dataframe.

Usage

create_final_filtered_dataframe(data = NULL, pon_threshold = 1, flagged_threshold = 1, soft_threshold = 0, hard_threshold = 0)

Arguments

data	dataframe containing the annotated SNV data (required)
pon_threshold	the number of recurrent normal samples a mutation is found in (default: 1)
flagged_threshold	the number of flagged filters a mutation is found in (default: 1)
soft_threshold	the maximum number of reads a mutation can be found in a soft clipped region (default: 0)
hard_threshold	the maximum number of reads a mutation can be found in a hard clipped region (default: 0)

Value

Returns a dataframe containing hard filtered SNVs.

Author(s)

Richard J. de Borja <[e-mail]>

shlienlab/ShlienLab.Core.SSM documentation built on May 20, 2019, 5:27 p.m.