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
Usage
Arguments
Value
View source: R/sampleSelection.R
Description
Select samples based on quantile of sample time distribution. Requires date to be at and of sequence label
Usage
1
time_stratified_sample(n, path_to_align, path_to_save = NULL)
Arguments
path_to_save
Where to store (as fasta) the filtered alignment
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.
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Description Usage Arguments Value
View source: R/sampleSelection.R
Description
Select samples based on quantile of sample time distribution. Requires date to be at and of sequence label
Usage
1 | time_stratified_sample(n, path_to_align, path_to_save = NULL)
|
Arguments
path_to_save |
Where to store (as fasta) the filtered alignment |
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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