R/spladder_parsing.R
spladder_transform.RdImports SplAdder output from a given path and transforms it into standardized junction format. Results from one patients should be stored per folder.
spladder_transform(path)The path to a folder with SplAdder output
A tibble in standardized junction format, combining all alternative splicing classes that are covered by SplAdder
path <- system.file("extdata", "", package = "splice2neo")
spladder_juncs <- spladder_transform(path)
#> Importing Spladder files ...
#> Importing Spladder files completed
spladder_juncs
#> # A tibble: 26 × 8
#> junction_start junction_end strand chromosome Gene class junc_id
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 896180 896673 + chr1 ENSG00000187961.… A3SS chr1:8…
#> 2 896180 897009 + chr1 ENSG00000187961.… A3SS chr1:8…
#> 3 889462 891303 - chr1 ENSG00000188976.… A3SS chr1:8…
#> 4 889903 891303 - chr1 ENSG00000188976.… A3SS chr1:8…
#> 5 763229 764383 + chr1 ENSG00000228794.… A5SS chr1:7…
#> 6 763233 764383 + chr1 ENSG00000228794.… A5SS chr1:7…
#> 7 934993 935072 - chr1 ENSG00000188290.… A5SS chr1:9…
#> 8 934993 935246 - chr1 ENSG00000188290.… A5SS chr1:9…
#> 9 764484 776580 + chr1 ENSG00000228794.… cass… chr1:7…
#> 10 776753 783034 + chr1 ENSG00000228794.… cass… chr1:7…
#> # ℹ 16 more rows
#> # ℹ 1 more variable: number_supporting_reads <dbl>