This file describes how to run the ARIEL script written by Jennifer Asimit
in the Applied Statistical Genetics group led by Eleftheia Zeggini at 
the Wellcome Trust Sanger Institute.

The analysis requires two source files:
1) ARIELqcc_script_general.R
2) ARIELqcc.R

The first script (ARIELqcc_script_general.R) is the only script that the user needs to call,
but the other script is necessary for the main script to work properly.  The scripts are 
written such that all the scripts need to be in the same directory as the data so that they can be found.

The main script (ARIELqcc_script_general.R) takes 6 input parameters:
1) Chromosome number to analyze (e.g. an interger between 1-22)
2) Minor Allele Frequency Cutoff for analysis (e.g. 0.05)
3) Genotype File Name
4) Phenotype File Name
5) Gene Definition File
6) Output File Name
7) Non-consensus Quality Score Indicator (1 for non-consensus scores, 0 for consensus scores) 

The Genotype File is a tab-delimited file with one line per SNP and 6+3N columns, where N is the number
of individuals being analyzed. An example Genotype File, data-example.txt.gz is provided within ariel.tar.gz. The columns must be in this order:
1) Chromosome
2) Position
3) ID
4) Reference Allele
5) Alternative Allele
6) consensus SNP Quality Score
7) Allele 1 for Individual 1 (1=alt allele, 0=ref allele)
8) Allele 2 for Individual 1 (1=alt allele, 0=ref allele)
9) Genotype Quality Score for Genotype of Individual 1 OR Non-consensus SNP Quality Score of Individual i
....and so on for each individual to analyze


The Phenotype File is a standard 6-column PLINK .fam file with individuals in the same order as the genotype file.
The 6 columns are:
1) Pedigree ID
2) Individual ID
3) Father ID
4) Mother ID
5) Sex
6) Case/Control Status


The Gene Definition File has the following 4 columns:
1) Gene name
2) Chromosome Number
3) Gene Start Position
4) Gene End Position

The script is called in the following manner from the command line:

>R CMD BATCH '--args arg_1 arg_2 arg_3 arg_4 arg_5 arg_6' ARIELqcc_general.R chr_<arg_1>_ARIEL_script.Rout

The output file is a tab-delimited file with 16 columns:
1)  Gene Name
2)  Total Number of Variants in Gene
3)  Chromosome
4)  Gene Start Position
5)  Gene Stop Position
6)  Number of Low Frequency Variants Analyzed in Gene
7)  Collapsing p-value
8)  ARIEL p-value
9)  Collapsing OR adjusted
10) ARIEL OR adjusted
11) Lower 95% Confidence Interval Collapsing OR adjusted
12) Lower 95% Confidence Interval ARIEL OR adjusted
13) Upper 95% Confidence Interval Collapsing OR adjusted
14) Upper 95% Confidence Interval ARIEL OR adjusted
15) Collapsing OR
16) ARIEL OR