buildFusionProteinDB: Create customized protein database from fusion events

Description Usage Arguments Value Examples

View source: R/dbCreator.R

Description

Create customized protein database from fusion events

Usage

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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

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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)

Shawn-Xu/PGA documentation built on Aug. 28, 2020, 9:58 p.m.