###init README.md

THIS SCRIPT determines if two alleles are significantly differentially translated given polysome profiling followed by digital droplet PCR data.

There are two required arguments:

1. --filename = the name of the input ddPCR file CC: We need to add the specifications for the file. How should it be formatted?
   
2. --expected_ratios = expected mutant/wildtype ratio (usually 1:1 for a diploid heterozygote)
   

Optional arguments include:

1. --fractions: a vector that specifies whether the groups analyzed will be the individual fractions or groups based on
   number of ribosomes
   Default value = NULL (groups generated will correspond to each individual polysome fraction)
   

CC: Note that the vector has to be comma separated

If vector is specified (i.e. ```7,3,1,1,1,5```), then the individual fractions will be further grouped based on number of ribosomes<br/>

2. --diff: a numeric value that specifies the maximum acceptable difference between inputted and calculated
   mutant/wildtype expected ratios
   Default value = 0.10 (10%) CC: I think this can be removed as it is simply a sanity check and warning message
   

3. --nsims: the number of boostrap simulations performed
   Default value = 1000
   

4. --output: filename of the output file (where the generated pvalues are)
   Default value = "output.csv", located in the same directory as this script
   

• Add one line that demonstrates the use case with a positive control example.
  
• Add a directory called example that would be the positive control test case.