Formats CI-SpliceAI with -t flag output and filter for predicted effects

Source: R/format_cispliceai.R

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.

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

Examples

cispliceai_file <- system.file("extdata", "cispliceai_thresh_output.vcf", package = "splice2neo")
df <- parse_cispliceai_thresh(cispliceai_file)
format_cispliceai_thresh(df)
#> # A tibble: 21 × 6
#>    mut_id                      effect score chr   pos_rel       pos
#>    <chr>                       <fct>  <dbl> <chr>   <int>     <int>
#>  1 chr2_152389953_T_A,C,G      DL      0.96 chr2        3 152389956
#>  2 chr2_152389953_T_A,C,G      DL      0.9  chr2        3 152389956
#>  3 chr2_152389953_T_A,C,G      DL      0.97 chr2        3 152389956
#>  4 chr2_179415988_C_CA         AL      1    chr2       -1 179415987
#>  5 chr2_179415988_C_CA         AG      0.05 chr2        0 179415988
#>  6 chr2_179415988_C_CA         AG      0.03 chr2        7 179415995
#>  7 chr2_179415988_C_CA         AG      0.04 chr2        9 179415997
#>  8 chr2_179446218_ATACT_A      DG      0.03 chr2      -11 179446207
#>  9 chr2_179446218_ATACT_A      DL      0.87 chr2        8 179446226
#> 10 chr2_179446218_ATACT_AT,ATA DG      0.05 chr2      -11 179446207
#> # ℹ 11 more rows