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Parse SARS-CoV-2 VOC/VOI Variant Metadata from Excel

Source: R/get_variants.R
get_variants.Rd

Reads a structured Excel workbook of SARS-CoV-2 Variants of Concern (VOC) and Variants of Interest (VOI) and returns a named list containing mutation profiles, nomenclature, temporal detection metadata, defining SNPs, and a fully citable reference table with interactive display support.

Usage

get_variants(tibble, check = FALSE)

Arguments

tibble

A tibble or data.frame produced by read_excel from SARS_CoV_2_VOC_VOI.xlsx. Column 1 must be the Variant field column; columns 2 onward are one column per variant in the order listed above.

check

Logical. If TRUE, validates that all internal vectors have equal length and stops with an informative message on mismatch. Default FALSE.

Value

A named list with 13 elements; see Details for full descriptions.

Details

Intended to be called once during data preparation via data-raw/sarscov2_variants.R:


  variants_dat  <- readxl::read_excel("SARS_CoV_2_VOC_VOI.xlsx")
  variants_list <- get_variants(variants_dat)
  saveRDS(variants_list,
          file = "inst/extdata/sarscov2_variants.rds")

The saved object can then be loaded anywhere in the package or vignettes:


  voc_data <- readRDS(system.file("extdata", "sarscov2_variants.rds",
                                  package = "ViralEntropR"))

Column order of variants in the Excel workbook: Alpha, Beta, Epsilon, Eta, Iota, Kappa, Delta, Lambda, Gamma, Zeta, Theta, Omicron.

Returned list elements:

WHO_Label

List. WHO variant label strings (e.g. "Alpha").

Pango_Lineage

List. Pango lineage designations.

GISAID_Clade

Character vector. GISAID clade strings.

Nextstrain_Clade

Character vector. Nextstrain clade strings.

Country_First_Detected

List. Country of first documented detection per variant.

Date_Earliest_Sample

Character vector. Month-Year of the earliest documented sample per variant.

Date_First_Detected

Character vector. Month-Year of world-level first detection.

Date_First_Detected_US

Character vector. Month-Year of first US detection.

Spike_Mutations

List. Spike protein mutation strings read from the Excel workbook.

Mutation_Sites

List. Integer site positions extracted from Spike_Mutations.

Defining_SNPs

List. Canonical defining SNP strings per variant (NA where not characterised).

Defining_SNP_Sites

List. Integer positions extracted from Defining_SNPs.

References

Named list with three elements: $data — data frame of 21 verified references; $display(variant = NULL) — interactive datatable, optionally filtered by WHO label; $cite(variant) — character vector of formatted citation strings suitable for manuscript use.