项目作者: hessJ

项目描述 :
Functional LD-interval EnrichmEnt Test -- biological interpretation of GWAS signals
高级语言: R
项目地址: git://github.com/hessJ/FLEET.git
创建时间: 2017-03-31T16:57:25Z
项目社区:https://github.com/hessJ/FLEET

开源协议:

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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

https://github.com/hessJ/FLEET/wiki

Download and install

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

Check for updates

  1. git pull

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

Run

  1. bash install.sh

Display help commands/options:

  1. fleet.R --help
  2. or
  3. fleet.R -h

Will print something like this:

  1. ==========================================================
  2. *
  3. * Functional LD-interval EnrichmEnt Test (FLEET)
  4. *
  5. * Jonathan L. Hess, PhD and Stephen J. Glatt, PhD (c) 2017
  6. *
  7. * SUNY Upstate Medical University, PsychGENe Lab
  8. *
  9. * Contact: hessjo@upstate.edu
  10. *
  11. * https://github.com/hessJ/FLEET
  12. *
  13. * GNU GENERAL PUBLIC LICENSE v3
  14. ===========================================================
  15. Start time: 2017-10-04 11:25:16
  16. Location of fleet: /Users/jonathanhess/Documents/FLEET/fleet.R
  17. Usage: /Users/jonathanhess/Documents/FLEET/fleet.R [options]
  18. Options:
  19. -G CHARACTER, --gwas=CHARACTER
  20. Path to GWAS summary statistics. Column headers are required. Allowed delim = sep, tab, or comma
  21. -O CHARACTER, --out=CHARACTER
  22. output file name [default = fleetOut]
  23. -R DOUBLE, --r2=DOUBLE
  24. R-squared threshold for linkage disequilibrium calculations [default = 0.6]
  25. -W INTEGER, --ld-window=INTEGER
  26. Size of window (kilobases) for calculating linkage disequilibrium [default = 1000]
  27. -S CHARACTER, --snp-field=CHARACTER
  28. SNP column header in GWAS file
  29. -P CHARACTER, --pcol=CHARACTER
  30. P-value column header in GWAS file
  31. --robust=DOUBLE
  32. Computing robust standard errors using White method (via vcovHC function in sandwich pkg) [default = TRUE]
  33. -N INTEGER, --nPerms=INTEGER
  34. Number of permutations to perform [default = 1000]
  35. -T INTEGER, --threads=INTEGER
  36. Number of cores for parallel operations [default = 1]
  37. -L CHARACTER, --label-annotations=CHARACTER
  38. Path to annotation table [default = /Users/jonathanhess/Documents/FLEET/annotations/annotation.txt]
  39. -D CHARACTER, --rd-annots=CHARACTER
  40. Path to .Rdata annotations [default = /Users/jonathanhess/Documents/FLEET/annotations/]
  41. -F DOUBLE, --annot-cnt=DOUBLE
  42. Minimum annotation count observed across LD-clumps [default = 10]
  43. -M LOGICAL, --fleet-prune-ref=LOGICAL
  44. Initiate LD-pruning step of 1KG reference data. Only needs to be run once. [default = TRUE]
  45. -A LOGICAL, --fleet-annotate=LOGICAL
  46. Annotate LD-clumps with bedtools [default = TRUE]
  47. -E LOGICAL, --fleet-enrichment=LOGICAL
  48. Perform enrichment analysis with weighted linear models [default = TRUE]
  49. --fleet-permutation=LOGICAL
  50. Perform enrichment analysis with permutation (randomizing annotations) [default = TRUE]
  51. --fast-permutation=LOGICAL
  52. Simple permutation analysis [default = FALSE]
  53. --robust-permutation=LOGICAL
  54. Permutation analysis that will sample variants from the MAF bin of target SNPs [default = FALSE]
  55. --speed=CHARACTER
  56. Change behavior of linear models (fast mode: SET becomes response variable, slow mode: Z-score becomes response variable) [default = fast]
  57. --pthres=CHARACTER
  58. Table with P-value threshold(s) for SNP bins [default P-values < 5e-08, 1e-07, and 1e-06]
  59. --plots=LOGICAL
  60. Turning this on will produce multiple plots to display summary statistics [default = FALSE]
  61. -h, --help
  62. Show this help message and exit

GNU GENERAL PUBLIC LICENSE v3

  1. This program is free software: you can redistribute it and/or modify
  2. it under the terms of the GNU General Public License as published by
  3. the Free Software Foundation, either version 3 of the License, or
  4. (at your option) any later version.
  5. This program is distributed in the hope that it will be useful,
  6. but WITHOUT ANY WARRANTY; without even the implied warranty of
  7. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  8. GNU General Public License for more details.
  9. You should have received a copy of the GNU General Public License
  10. 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