cluster_muts: Computes mutations for sequences within specified clusters

In emvolz-phylodynamics/variantAnalysis: sarscov2 variant analysis

Description

Also derives defining mutations by contrasting with closest ancestor

Usage

cluster_muts(
  scanner_env,
  nodes = NULL,
  mutdata = list.files(patt = "cog_global_[0-9\\-]+_mutations.csv", full.name = TRUE,
    path = "../phylolatest/metadata/"),
  mut_variable = c("variants", "mutations"),
  min_seq_contrast = 1,
  overlap_threshold = 0.9,
  ncpu = 1
)

Arguments

scanner_env	output of scanner
nodes	integer vector of nodes for which results will be computed. Computes for all nodes in Y if omitted
mutdata	path to file or data frame with variant information
mut_variable	Name of variable in data frame (spec by mutfn) which contains genetic variant data
ncpu	number of CPUs for parallel processing

emvolz-phylodynamics/variantAnalysis documentation built on Nov. 13, 2021, 7:16 p.m.