call_mutations: Identify Sample Amino Acid Changes

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

Description

Function to identify full set of amino acid changes in a given sample (includes changes based on both SNVs and indels)

Usage

call_mutations(
  sample.dir,
  min.alt.freq = 0.01,
  name.sep = "NULL",
  reference = "https://raw.githubusercontent.com/mikesovic/IDI-AMSL/main/SC2_ref.tsv",
  write.mut.table = FALSE
)

Arguments

sample.dir	Path to directory with one tab-delimited file for each sample to analyze. Each file should contain columns named POS, REF, ALT, AF, DP and is generally a summary from a vcf file. Additional columns can be included and will be ignored. POS = genomic position, REF = reference base, ALT = alternate base/allele, AF = alt frequency, DP = read depth at site
min.alt.freq	Minimum frequency (0-1) for retaining alternate allele. Default = 0.01.
name.sep	Character in sample names that separates the unique sample identifier (characters preceeding the separator) from any additional text. Only text preceeding the first instance of the character will be retained.
reference	Reference genome information in MixVir format.
write.mut.table	Logical to indicated whether to write a text file that stores all mutations for all samples analyzed to working directory. This is the same information contained in data frame 'samp_mutations' created by this function. Default = FALSE

Value

Data frame 'samp_mutations' containing amino acid changes observed for each sample.

Examples

call_mutations()

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