calcparafun: Calculating global parameters

In ruy204/FiTnEss: FiTnEss: Finding TnSeq Essential Genes

Description

This function is part of fitnessRun function, where global parameters describing non-essential genes are being calculated.

In this step, usable tally files prepared in tallyprepfun were imported, and global parameters were estimated with minimized Cramer-von Mises value.

Usage

calcparafun(strain,usable_tally_list,save_location,rep_time)

Arguments

strain	strain name
usable_tally_list	output of self_tallyprepfun, usable tally files that prepared using raw tally and supporting files
save_location	path and name of where to save final results file, e.g. "/home/results_folder/results.xlsx"
rep_time	same argument of repeat_time from main function. Define how many times to run the pipeline in order to obtain best results: by default, we run 3 times.

Examples

calcparafun("PA14",usable_tally,
            "/home/TnSeq/results/results.xlsx",rep_time=5)

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