base_count: Retrieves the total number of observed unique bases.
In dieterich-lab/JACUSA2helper: Post-processing for JACUSA2 output

base_count

R Documentation

Retrieves the total number of observed unique bases.

Description

Retrieves the total number of observed unique bases. If ref is provided, reference base will be considered for counting, e.g.: At some site only base 'A' was observed but the reference was 'T'. base_count will be:

1, when ref is NOT provided, or
2, when ref is provided.

Usage

base_count(bases, ref = NULL)

Arguments

`bases`	vector of base calls or tibble of base call counts.
`ref`	vector of strings with reference bases

Value

numeric vector of total number of bases.

Examples

bc <- c("A", "AG", "C")
str(base_count(bc))

# use default observed base calls and condsider reference base
ref <- c("A", "A", "T")
str(base_count(bc, ref))

dieterich-lab/JACUSA2helper documentation built on March 1, 2023, 12:09 a.m.