Eqmr-fcfdr

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Contents

Introduction

The eqmr-fcfdr program allows to perform permutations and estimate the FDR.

Options

Short Long Description
-d --data The database (.db file)
-f --feature The feature database (.fdb file)
-r --cisdb The result database (.res file)
-c --cutoff The cutoff file for the summary statistic (BF or pval)
-w --window The cis-candidate window size in bp (default 500000)
-p --permut-dir The permutation directory
-b --permut-size The number of permutations
-s --cis-bin A string provided the number of bins per cis region separated by semi-colon (e.g. 50;10;50)
-q --qvalue The FDR value for which to get the p-value cut-off(s)
-c --chrom The name(s) of the chromosome(s) to focus on
--pval Compute FDR for p-value
--best Compute gene FDR by picking the best SNP for each gene

Examples

Here is an example of a configuration file with cutoffs:

$ cat PvalCutoff.txt
1.e-6
1.e-7
1.e-8

We can launch the program with the following command:

$ eqmr-fcfdr -d data.db -f genes.fdb -r results_cisreg.fcis --cutoff PvalCutoff.txt -b 10 --pval --best -w 500000 -p permutations -o results_fdr.summary

Here is how the output looks like:

$ cat results_fdr.summary
Pval    #Obs    #Perm   #N_perm  FDR
1.e-6   201     248     10       1.233831e-01
1.e-7   169     187     10       1.106509e-01
1.e-8   139     131     10       9.424460e-02


See Also

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Facts about Eqmr-fcfdrRDF feed
Main source filewarning.png"{{{mainsourcefile}}}" cannot be used as a page name in this wiki.
Program categoryData Analysis  +
Program languageC  +
Program nameeqmr-fcfdr  +
Program titleSummary of cis-regression results
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