Eqmr-fcrout

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Contents

Introduction

The eqmr-fcrout program takes as input the databases from eqmr-db, eqmr-fdb and eqmr-fcr, and returns as output the cis-regression results in plain text. It creates an output directory with as many files as the number of chromosomes. Each file is tabulated with the following format:


Options

Short Long Description
-d --data The database (.db file)
-f --feature The feature database (.fdb file)
-r --cisdb The result database (.fcis file)
-o --output The output directory
-w --window The cis-candidate window size in bp (default 500000)
-t --threshold Threshold on the Bayes Factor (or p-value if --pval)
-s --snp-file A one column file providing the name of the polymorphisms for which to get the results
-g --feature-table A table of features to extract
--best-snp Output only the best SNP(s) per feature
--pval Use p-value instead of Bayes Factor for thresholding


Examples

We can access a short help with the following command:

$ eqmr-fcrout --help
eqmr-fcrout - version 2.1
Copyright (C) 2008,2009 Jean-Baptiste Veyrieras (University of Chicago)
eqmr-fcrout comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.

--help	Display a brief help on program usage
--verbose	Output message on standard output to see what the program is doing
--best-snp	Output only the best SNP(s) per feature
--pval	Use p-value instead of Bayes Factor for thresholding

--data or -d	The database (.db file)
--feature or -f	The feature database (.fdb file)
--cisdb or -r	The result database (.res file)
--output or -o	The output file
--window or -w	The cis-candidate window size in bp (default 500kb)
--threshold or -t	Threshold on the snp Bayes Factor (on p-value if --pval activated)
--snp-file or -s	A one column file providing the name of the SNPs for which to get the results
--feature-table or -f	A feature table to focus on

Now, let’s assume we want the best SNP per feature for which the Bayes factor is greater than 100. We will run the following command:

$ eqmr-fcrout -d data.db -f features.db -r cisreg.fcis -t 100 --best-snp -o cisreg_res_bestsnp


Remarks



See Also

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