format_spliceai: Formats spliceAI output and filter for predicted effects

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

Formats spliceAI output and filter for predicted effects

Description

Reformat the data for each annotated effect per row, filters effects to have a probability score not NA and score > 0, and removes gene symbol from data to make non-redundant output.

Usage

format_spliceai(spliceai_variants, gene_table = NULL)

Arguments

spliceai_variants	tibble with parsed spliceAI mutations from parse_spliceai
gene_table	optional tibble with the columns: gene_id: ENSEMBL gene id gene_name: gene symbol

Value

A tibble with splicing effects per row. If gene_table is provided, the formatted data contains a column with the gene_id.

See Also

parse_spliceai, annotate_mut_effect

Examples

spliceai_file <- system.file("extdata", "spliceai_output.vcf", package = "splice2neo")
df <- parse_spliceai(spliceai_file)
format_spliceai(df)

TRON-Bioinformatics/splice2neo documentation built on July 27, 2024, 3:25 a.m.