buildFusionProteinDB {PGA} | R Documentation

## Create customized protein database from fusion events

### Description

Create customized protein database from fusion events

### Usage

    buildFusionProteinDB(x, genome = Hsapiens,
      fusion_method = "STAR-Fusion", max_nt = 100, out_dir = "./",
      prefix = "fusion", translating_method = "six_frame",
      min_aa_length = 10)

### Arguments

`x` | A tsv format file which contains fusion events.
`genome` | Genome information. This is a BSgenome object(e.g. Hsapiens).
`fusion_method` | Fusion calling method, default is "STAR-Fusion"
`max_nt` | The max length of DNA sequences to be extracted for each side, default is 60
`out_dir` | Output directory
`prefix` | The prefix of output files
`translating_method` | Translating DNA to protein (six_frame,three_frame, longest), default is six_frame.
`min_aa_length` | The minimum length of proteins, default is 10 aa.

### Value

The database file

### Examples

    fusion_file <- system.file("extdata/fusion/", "star-fusion_example_input.tsv",package="PGA")
    # This example input was downloaded from STAR-Fusion website (https://github.com/STAR-Fusion/STAR-Fusion/wiki)
    library("BSgenome.Hsapiens.UCSC.hg19")  # or library("BSgenome.Hsapiens.UCSC.hg38")
    res <- buildFusionProteinDB(fusion_file, genome=Hsapiens)

[Package PGA version 1.20.0 Index]