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Find taxa by haplotype IDs

Source: R/class_all_generics.R, R/class_phg_dataset.R
findSamplesByHaplotype.Rd

Return taxa IDs that contain a provided haplotype ID in rPHG2-related datasets.

Usage

findSamplesByHaplotype(object, ...)

# S4 method for class 'PHGDataSet'
findSamplesByHaplotype(object, hapIds = NULL, returnType = c("list", "tibble"))

Arguments

object

an rPHG2 dataset

...

Additional arguments, for use in specific methods

hapIds

A collection of unique haplotype IDs to query. If more than one haplotype ID is to be queried, please use a character vector.

returnType

How do you want to results returned? Options are:

  • "list" for a list of haplotype ID keys and character vectors of taxa IDs,

  • "tibble" for a tibble dataframe object that contains haplotype ID, taxa IDs, and the number of taxa found for each queried haplotype ID