id_snps: ID SNV-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 associated with single nucleotide variation. Changes associated with indels are identified in separate function. Used by call_mutations function.

Usage

id_snps(variant.calls, ref)

Arguments

variant.calls	Data frame with cols POS, REF, ALT, AF (alt freq), DP (total read depth). 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_snps()

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