circHunter_simulate: Simulation function

In datngu/CircRNA_simulator: An R package to simulate circRNA sequencing data

Description

This function used to simulate both circRNA and tandem RNA RNA sequencing data base on given information.

Usage

circHunter_simulate(
  BSJ_Info,
  tandem_rate = 0,
  error_rate = 0.005,
  set.seed = 2018,
  gtfSqlite,
  genomeFastaFile,
  txFastaFile,
  out_name = "circHunter_simuation",
  out_dir = "./",
  ...
)

Arguments

BSJ_Info	a data frame that contains 5 columns which are: Chr, start_EXONSTART, end_EXONEND, GENEID and cCount. Chr is chromosome name with formated as 1:22, X, Y, Mt. start_EXONSTART is starting position starting exon of circRNA, end_EXONEND is ending position ending exon of circRNA, GENEID is gene ID contains circRNA (used to get gene model) and cCount are number of read pair want to generated for the target circRNA.
tandem_rate	the rate tandem RNA that you wish to simulated eg. 0.05
error_rate	sequencing error rate, defaut is 0.005
set.seed	set seed for reproducibility, defaut is on with 2018
gtfSqlite	path to your annotation file, Sqlite formated (generated by GenomicFeatures)
genomeFastaFile	path to your genome fasta file
txFastaFile	path to your transcript fasta file (cDNA)
out_name	prefix output folders, defaut is "circHunter_simuation"
out_dir	the directory contains output, defaut is the current derectory

datngu/CircRNA_simulator documentation built on Feb. 22, 2020, 12:19 a.m.