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.
https://github.com/hessJ/FLEET/wiki
git clone https://github.com/hessJ/FLEET
git pull
A description of the method is provided in the powerpoint slides (fleet_slides.ppt).
bash install.sh
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
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/>.
========================================================================
Made on a MacBook Pro Retina, 2.5 GHz Intel Core i7, 16 GB 1600 MHz DDR3