format_cispliceai_thresh: Formats CI-SpliceAI with -t flag output and filter for...

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

Formats CI-SpliceAI with -t flag 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_cispliceai_thresh(cispliceai_variants, transcripts_gr = NULL)

Arguments

cispliceai_variants	tibble with parsed CI-SpliceAI mutations from parse_spliceai
transcripts_gr	Optionally, A GRanges object with transcript ranges created by GenomicFeatures::transcripts(txdb)can be provided which will allow to annotate full gene ids to the formatted table and to consider only transcripts related to the annotated gene in annotate_mut_effect. This parameter is optionally.

Value

A tibble with splicing effects per row

See Also

parse_cispliceai_thresh, annotate_mut_effect

Examples

cispliceai_file <- system.file("extdata", "cispliceai_thresh_output.vcf", package = "splice2neo")
df <- parse_cispliceai_thresh(cispliceai_file)
format_cispliceai_thresh(df)

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