variants: An R6 class representing haploid variants from a reference...

Description Usage Format Value Connections to ref_genome objects Methods See Also

Description

This class should NEVER be created using variants$new. Only use create_variants. This class wraps a pointer to a C++ object, which is why there are no fields to manipulate directly. All manipulations are done through this class's methods.

Usage

1

Format

An R6Class generator object

Value

An object of class variants.

Connections to ref_genome objects

Regarding the ref_genome object you use to create a variants object, you should note the following:

Methods

Viewing information:

ptr()

View the pointer to the variant information. This is used internally by jackalope and shouldn't be of much use to users.

n_chroms()

View the number of chromosomes.

n_vars()

View the number of variants.

sizes(var_ind)

View vector of chromosome sizes for a given variant.

chrom_names()

View vector of chromosome names.

var_names()

View vector of variant names.

chrom(var_ind, chrom_ind)

View a chromosome sequence string based on indices for the chromosome (chrom_ind) and variant (var_ind).

gc_prop(var_ind, chrom_ind, start, end)

View the GC proportion for a range within a variant chromosome.

nt_prop(nt, var_ind, chrom_ind, start, end)

View the proportion of a range within a variant chromosome that is of nucleotide nt.

Editing information:

set_names(new_names)

Set names for all variants. new_names is a character vector of what to change names to, and it must be the same length as the # variants.

add_vars(new_names)

Add new, named variant(s) to the object. These variants will have no mutations. If you want to add new variants with mutations, either re-run create_variants or use the dup_vars method to duplicate existing variants.

dup_vars(var_names, new_names = NULL)

Duplicate existing variant(s) based on their name(s). You can optionally specify the names of the duplicates (using new_names). Otherwise, their names are auto-generated.

rm_vars(var_names)

Remove one or more variants based on names in the var_names vector.

add_sub(var_ind, chrom_ind, pos, nt)

Manually add a substitution for a given variant (var_ind), chromosome (chrom_ind), and position (pos). The reference nucleotide will be changed to nt, which should be a single character.

add_ins(var_ind, chrom_ind, pos, nts)

Manually add an insertion for a given variant (var_ind), chromosome (chrom_ind), and position (pos). The nucleotide(s) nts will be inserted after the designated position.

add_del(var_ind, chrom_ind, pos, n_nts)

Manually add a deletion for a given variant (var_ind), chromosome (chrom_ind), and position (pos). The designated number of nucleotides to delete (n_nts) will be deleted starting at pos, unless pos is near the chromosome end and doesn't have n_nts nucleotides to remove; it simply stops at the chromosome end in this case.

See Also

create_variants


jackalope documentation built on Dec. 1, 2019, 1:17 a.m.