Command line tools - Half-life calculation


Combined with the arguments for data loading and normalizing you can use the flags described below for the final half-life calculations.

List of necessary flags

Since you can use an unlimited number of different half-life calculations, you can use the flag -h followed by the number of the current calculation for doing several methods at once.
-h1 method First method for calculation of half-lives (e.g. 'pre' for pre-existing/total based, 'new' for newly transcribed/total based or 'new/pre' for newly transcribed/pre-existing based calculations)
...
-hn method n-th method for half-life calculation
-t time Labeling time point for which calculation will be done

List of optional flags

-plot BOOLEAN TRUE if half-life calculations should be plotted.
-bias BOOLEAN TRUE if bias correction should be performed and used before half-life calculation. For this method to work you have to also use the -R, -ur and -ufo flags.
-corr numerical The half-life median that will be used for median-based correction factor calculation; for '-corr -1' the median will be calculated from your half-life calculations
-o filename Name of the file in which the half-life values will be written
-w printing information Which information will be printed: 'halflife', 'ratio' or 'both'
-m methods The half-life calculation methods whose results should be included in the output; these methods have to be a subset of the previously defined methods for calculation. If no list of methods is specified, every calculation will be printed. The methods are called pre, new and new/pre (see above); for more than one method please separate the methods with commas (e.g. '-m pre,new')
For the printing of your output you have to use the flags -o, -w and -m combined.

Example call

-i data.txt -ct totalRNA2 -cp preexistingRNA2 -cn newlytranscribed_HumanExon2 -l standard -h1 new -h2 pre -h3 new/pre -t 60 -o halflives.txt -w halflife -m new,pre,new/pre

HALO documentation