mutation_prevalence: Compute prevalence of mutations

In arisp99/s3examples: What the Package Does (One Line, Title Case)

Description

Generate a table representing the prevalence of unique mutations. In order to ensure confidence in the results, a threshold is provided indicating confidence in genotype calls. All data that do not meet this threshold will be removed from the computation.

Usage

mutation_prevalence(data, threshold)

Arguments

data	A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr).
threshold	A minimum UMI count which reflects the confidence in the genotype call. Data with a UMI count of less than the threshold will be filtered out from the analysis.

Value

A tibble with the extra class mutation_prev. The output has the following columns:

• mutation_name: The unique mutation sequenced.

• n_total: The number of samples for which a mutation site was sequenced.

• n_mutant: The number of samples for which a mutation occurred.

• prevalence: The prevalence of the mutation.

arisp99/s3examples documentation built on Jan. 15, 2022, 11:11 a.m.