buildFusionProteinDB: Create customized protein database from fusion events

In Shawn-Xu/PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

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)

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