buildFusionProteinDB: Create customized protein database from fusion events

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

Create customized protein database from fusion events

Description

Create customized protein database from fusion events

Usage

buildFusionProteinDB(x, species = "Homo sapiens",
  genome_version = "hg38", 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.
species	Species, default is "Homo sapiens"
genome_version	Genome version, default is "hg38"
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)
res <- buildFusionProteinDB(fusion_file,genome_version="hg19")

wenbostar/PGA documentation built on March 24, 2022, 6:48 p.m.