FLEET

Functional LD-interval EnrichmEnt Test (active development, i.e., easy to break)

This tool is used for biological interpretation of GWAS signals for polygenic phenotypes.

Please visit the Wiki page to set up FLEET on your workstation

Download and install

 git clone https://github.com/hessJ/FLEET

Check for updates

 git pull

A description of the method is provided in the powerpoint slides (fleet_slides.ppt).

Run

bash install.sh

Display help commands/options:

fleet.R --help 
    or
fleet.R -h

Will print something like this:


==========================================================
*
* Functional LD-interval EnrichmEnt Test (FLEET)
*
* Jonathan L. Hess, PhD and Stephen J. Glatt, PhD (c) 2017
*
* SUNY Upstate Medical University, PsychGENe Lab
*
* Contact: hessjo@upstate.edu
*
* https://github.com/hessJ/FLEET
*
* GNU GENERAL PUBLIC LICENSE v3
===========================================================
Start time: 2017-10-04 11:25:16
Location of fleet: /Users/jonathanhess/Documents/FLEET/fleet.R
Usage: /Users/jonathanhess/Documents/FLEET/fleet.R [options]
Options:
    -G CHARACTER, --gwas=CHARACTER
        Path to GWAS summary statistics. Column headers are required. Allowed delim = sep, tab, or comma
    -O CHARACTER, --out=CHARACTER
        output file name [default = fleetOut]
    -R DOUBLE, --r2=DOUBLE
        R-squared threshold for linkage disequilibrium calculations [default = 0.6]
    -W INTEGER, --ld-window=INTEGER
        Size of window (kilobases) for calculating linkage disequilibrium [default = 1000]
    -S CHARACTER, --snp-field=CHARACTER
        SNP column header in GWAS file
    -P CHARACTER, --pcol=CHARACTER
        P-value column header in GWAS file
    --robust=DOUBLE
        Computing robust standard errors using White method (via vcovHC function in sandwich pkg) [default = TRUE]
    -N INTEGER, --nPerms=INTEGER
        Number of permutations to perform [default = 1000]
    -T INTEGER, --threads=INTEGER
        Number of cores for parallel operations [default = 1]
    -L CHARACTER, --label-annotations=CHARACTER
        Path to annotation table [default = /Users/jonathanhess/Documents/FLEET/annotations/annotation.txt]
    -D CHARACTER, --rd-annots=CHARACTER
        Path to .Rdata annotations [default = /Users/jonathanhess/Documents/FLEET/annotations/]
    -F DOUBLE, --annot-cnt=DOUBLE
        Minimum annotation count observed across LD-clumps [default = 10]
    -M LOGICAL, --fleet-prune-ref=LOGICAL
        Initiate LD-pruning step of 1KG reference data. Only needs to be run once. [default = TRUE]
    -A LOGICAL, --fleet-annotate=LOGICAL
        Annotate LD-clumps with bedtools [default = TRUE]
    -E LOGICAL, --fleet-enrichment=LOGICAL
        Perform enrichment analysis with weighted linear models [default = TRUE]
    --fleet-permutation=LOGICAL
        Perform enrichment analysis with permutation (randomizing annotations) [default = TRUE]
    --fast-permutation=LOGICAL
        Simple permutation analysis [default = FALSE]
    --robust-permutation=LOGICAL
        Permutation analysis that will sample variants from the MAF bin of target SNPs [default = FALSE]
    --speed=CHARACTER
        Change behavior of linear models (fast mode: SET becomes response variable, slow mode: Z-score becomes response variable) [default = fast]
    --pthres=CHARACTER
        Table with P-value threshold(s) for SNP bins [default P-values < 5e-08, 1e-07, and 1e-06]
    --plots=LOGICAL
        Turning this on will produce multiple plots to display summary statistics [default = FALSE]
    -h, --help
        Show this help message and exit

GNU GENERAL PUBLIC LICENSE v3

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses></http:>.

========================================================================

Made on a MacBook Pro Retina, 2.5 GHz Intel Core i7, 16 GB 1600 MHz DDR3