Description Usage Arguments Examples
Single function to run whole FiTnEss: from tally files to final results
1 2 3 | FiTnEss_Run(strain,file_location,permissive_file,
homologous_file,gene_file,save_location,
repeat_time=3)
|
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 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.