format_pangolin: Formats pangolin output and filter for predicted effects

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

Formats pangolin output and filter for predicted effects

Description

Reformat the data for each annotated effect per row. As pangolin does not provide information on donor or acceptor, use both for gain and loss annotations. Effects with score = 0 are filtered out. The resulting score represents the absolute value of the Pangolin score.

Usage

format_pangolin(variants, keep_gene_id = FALSE)

Arguments

variants	tibble with parsed pangolin mutations from parse_pangolin
keep_gene_id	Indicator whether the gene_id should be kept in the formatted data (default: FALSE).

Value

A tibble with splicing effects per row

pangolin_file <- system.file("extdata", "spliceai_output.pangolin.vcf", package = "splice2neo") df <- parse_pangolin(pangolin_file) format_pangolin(df)

See Also

parse_spliceai, annotate_mut_effect, format_spliceai

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