region_time_stratified_sample: Select a random sample from aligment stratified through time...

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

Description

Select samples based on quantile of sample time distribution. Requires date to be at and of sequence label. Alternatively can do a simple random sample within a region

Usage

region_time_stratified_sample(
  region_regex,
  n,
  path_to_align,
  D = NULL,
  nregion = NULL,
  path_to_save = NULL,
  time_stratify_region = TRUE
)

Arguments

region_regex	Sample names matching this regular expression will be retained and closest matches also retained
n	sample size from outside region
D	An optional distance matrix between sequences. Can be based on cophenetic distance from ML tree. If not provided will compute using a HKY model (slow!)
nregion	sample size within region; if null will include everything in region
path_to_save	Where to store (as fasta) the filtered alignment
time_stratify_region	If TRUE (default) will perform a time stratified sample within region, otherwise will do a simple random sample
q_threshold	Clock outlier threshold
minEdge	minimum branch length (substitutions per site) to stabilize clock inference

Value

A DNAbin alignment. Will also save to path_to_save

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