id_indels: ID Indel-based Amino Acid Changes

In mikesovic/MixviR_v1: Explore Viral Variation In Mixed Sample Short Read Sequence Data - Esp Sars-Cov2

Description

Identify amino acid changes associaged with indel variation. Changes associated with SNVs are identified in separate function. Used by call_mutations function.

Usage

id_indels(variant.calls, ref)

Arguments

variant.calls	Data frame with cols POS, REF, ALT, AF, DP. Additional columns will be ignored.
ref	reference genome in "MixVir" format (genomic positions repeated for each associated feature they're associated with, etc.)

Value

Data frame with cols "genomic_pos", "ref_base", "gene", "ref_codon", "ref_AA", "gene_aa_position", "ref_identity", "REF", "ALT", "ALT_freq", "ALT_COUNT", "samp_codon", "samp_AA", "samp_identity", "DP"

Examples

id_indels()

mikesovic/MixviR_v1 documentation built on Dec. 21, 2021, 6:56 p.m.