is_indel_method: Add a column to state whether the variant is an indel or not

In vladimirsouza/lrRNAseqBenchmark: Figure out how to call varaints from Iso-Seq data

Add a column to state whether the variant is an indel or not

Description

To classify the variant as an indel, first the function looks at the VCF file of the 'first_method'. If the variant is not there, if looks at the VCF file of the 'second_method'.

Usage

is_indel_method(input_table, first_method, second_method = NULL)

Arguments

input_table	A data.frame. The master table to add the new column.
first_method	A 1-length string. The name of the first method.
second_method	A 1-length string. The name of the second method

Details

Output meaning: * ‘-1' means that the variant type couldn’t be defined, because it is heterozygous alternative; * '0' means it is not an indel; * '1' means it is an indles; * ‘NA' means the 'first_method' (and the 'second_method') didn’t call the variant.

Value

A data.frame.

vladimirsouza/lrRNAseqBenchmark documentation built on March 23, 2023, 7:32 a.m.