format_spliceai: Formats spliceAI output and filter for predicted effects

View source: R/format_spliceai.R

format_spliceaiR Documentation

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 Nov. 9, 2024, 5:28 p.m.