construct_haplotypes: Given a set of sequences, extract the haplotypes.
In philliplab/ViralHaplotyper: Viral Haplotyper

Description Usage Arguments Details Value

Various different methods can be used to construct the haplotypes. The following are currently implemented:

unique - Each unique sequence is a haplotype
single - The entire dataset is a single haplotype

1 2	construct_haplotypes(seq_data, cluster_method = "unique", cluster_params = list(NULL), n_header_letters = 1)

`seq_data`	The input data
`cluster_method`	The clustering method to use when constructing the haplotypes
`cluster_params`	A list of input parameters to the clustering algorithm.
`n_header_letters`	The number of letters to take from a FASTA header of one of the sequences and prepend to the haplotype name.

The haplotypes are assigned names by taking the first n letters from the name of a random sequence (the sequence names should all be the same for the first n letters) and appending _hapx to it. Where is a number the that keeps track of the haplotype numbers.

A list of objects of class Haplotype-class

philliplab/ViralHaplotyper documentation built on May 25, 2019, 5:05 a.m.