filter_quality1: Selects a background reference set of sequences with good...

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

- sequences with poor relationship with a molecular clock - optionally deduplicate identical sequences

Usage

filter_quality1(
  path_to_align,
  fn_tree = NULL,
  path_to_save = NULL,
  q_threshold = 0.05,
  minEdge = 1/29000/10,
  deduplicate_identical = TRUE,
  ncpu = 6,
  collapse_D = 1/29000/2
)

Arguments

fn_tree	Optional path to a maximum likelihood tree OR a ape::phylo. If not provided, will estimate using fasttree.
path_to_save	Where to store (as RDS) the filtered alignment etc
q_threshold	Clock outlier threshold
minEdge	minimum branch length (substitutions per site) to stabilize clock inference
deduplicate_identical	if TRUE, will only include one sequence (most recent) from among sets of identical sequences
collapse_D	Any distances less than this value will be treated as zero

Value

Writes a RDS file containing filtered aligment, time tree, fasttree, and sample times. Return value is a list with the same

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.