Formats pangolin output and filter for predicted effects

Source: R/format_pangolin.R

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.

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)