FiTnEss_function: Run FiTnEss

In ruy204/FiTnEss: FiTnEss: Finding TnSeq Essential Genes

Description

Single function to run whole FiTnEss: from tally files to final results

Usage

FiTnEss_Run(strain,file_location,permissive_file,
            homologous_file,gene_file,save_location,
            repeat_time=3)

Arguments

strain	name of the strain
file_location	path and name of tally file for run, e.g. '/home/your_folder/your_tally.txt'
permissive_file	path and name of non-permissive TA site file that generated from genomic pre-processing step
homologous_file	path and name of homologous TA site file that generated from pre-processing step
gene_file	path and name of GFF3 gene file that downloaded from [Pseudomonas Genome Database](http://www.pseudomonas.com/strain/show?id=109)
save_location	path and name of where to save final results file
repeat_time	how many times to run the pipeline in order to obtain best results: by default, we run 3 times

Examples

1. install FiTnEss package from github using devtools

devtools::install_github("ruy204/FiTnEss")

#2. load packages

require(FiTnEss)
library(dplyr)
library(tidyr)
library(openxlsx)

#3. run FiTnEss

FiTnEss_Run("UCBPP",
            "/home/TnSeq/data/test_data/PA14_M9_rep1_tally.txt",
            "/home/TnSeq/data/test_data/nonpermissive_TA_sites.txt",
            "/home/TnSeq/data/test_data/homologous_TA_sites.txt",
            "/home/TnSeq/data/test_data/PA14_gene_file.txt",
            "/home/TnSeq/test_result/test_results.xlsx",
            repeat_time = 3)

ruy204/FiTnEss documentation built on Jan. 23, 2021, 2:52 a.m.