NAME

       QTLtools fdensity - Functional density around molecular QTLs

SYNOPSIS

       QTLtools  fdensity  --qtl  significant_genes.bed  --bed TFs.encode.bed.gz --out output.txt
       [OPTIONS]

DESCRIPTION

       This mode measures the density of functional annotations around the genomic  positions  of
       molecular  QTLs.  The method is detailed in <https://www.nature.com/articles/ncomms15452>.
       In brief, we first enumerate all annotations within a given window  around  the  molecular
       QTLs  (by  default  1 Mb).   Then, we split this window into small bins (default 1 kb) and
       count the number of  functional  annotations  overlapping  each  bin.   This  produces  an
       annotation count per bin that can be then plotted to see if there is any peak or depletion
       around the molQTLs.

OPTIONS

       --qtl in.bed
              List of QTLs of interest in BED format.  REQUIRED.

       --bed functional_annotation.bed.gz
              Functional annotations in BED format.  REQUIRED.

       --out output.txt
              Output file.  REQUIRED.

       --window integer
              Window size around the molecular QTL position.  DEFAULT=1000000

       --bin integer
              Bin size in base pairs.  DEFAULT=1000

INPUT FILES

       --qtl file
        List of QTLs of interest.  An example:

        1    15210     15211     1_15211   ENSG00000227232.4   -
        1    735984    735985    1_735985  ENSG00000177757.1   +
        1    735984    735985    1_735985  ENSG00000240453.1   -
        1    739527    739528    1_739528  ENSG00000237491.4   +

        The column definitions are:

        1   The variant chromosome
        2   The variant's start position (0-based)
        3   The variant's end position (1-based)
        4   The variant ID
        5   The phenotype ID (not used)
        6   The phenotype's strand.

       --bed file
        List of annotations in BED format.  An example:

        1    254874    265487
        1    730984    735985
        1    734984    736585
        1    739527    748528

        The column definitions are:

        1   Chromosome
        2   Start position (0-based)
        3   End position (1-based)

OUTPUT FILE

       --out file
        Space separated results output file detailing the enrichment with the following columns:

        1   The start position of the bin
        2   The end position of the bin
        3   The number of associations in this bin

EXAMPLE

       1 You need to prepare a BED file containing the positions of the QTLs of interest.  To  do
         so,  extract all significant hits at a given FDR threshold (e.g. 5%), and then transform
         the significant QTL list into a BED file:

         Rscript ./script/qtltools_runFDR_cis.R results.genes.full.txt.gz 0.05 results.genes
         cat results.genes.significant.txt | awk '{ print $9, $10-1, $11, $8, $1, $5 }' | tr '  '
         '\t' | sort -k1,1V -k2,2g > results.genes.significant.bed

       2 Measure the density using the following command:

         QTLtools  fdensity  --qtl  results.genes.significant.bed  --bed  TFs.encode.bed.gz --out
         density.TF.around.QTL.txt

SEE ALSO

       QTLtools(1)

       QTLtools website: <https://qtltools.github.io/qtltools>

BUGS

       Please submit bugs to <https://github.com/qtltools/qtltools>

CITATION

       Delaneau, O., Ongen, H., Brown, A. et al. A complete tool set for molecular QTL  discovery
       and analysis. Nat Commun 8, 15452 (2017).  <https://doi.org/10.1038/ncomms15452>

AUTHORS

       Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)