==GREGOR==

'''GREGOR''' ('''G'''enomic '''R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.

Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.

== Get GREGOR Source Codes ==

=== Download from webpage ===
Through this link [http://csg.sph.umich.edu/GREGOR/ GREGOR], you can download a copy of GREGOR.

== Build GREGOR ==

To build GREGOR, copy the GREGOR package to the directory you want, and then run the following command:

tar xzvf GREGOR.tar.gz

After you unzip, you can find 3 directories in "GREGOR" (./example ./lib ./script).

== Download reference files ==

Download the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download], then un-package the file

tar xzvf GREGOR.ref.tar.gz

After unzip, you will get 47 reference files in the directory "~/ref"

== Basic Usage Example ==

When you run

perl GREGOR.pl

you will get some information about GREGOR

----------------------------------------------------------------------------------
GREGOR.pl : Functional annotation of trait-associated variants
----------------------------------------------------------------------------------
This program tests for enrichment of an input list of trait-associated index
SNPs ([chr:pos] format or rsID, hg19) in experimentally annotated regulatory
domains (BED files).

Note: the index SNPs should be hg19 version. All maf and LD data are from 1000G
EUR samples! (Release date : May 21, 2011)

Version : 1.1.0

Report Bug(s) : jich[at]umich[dot]edu
----------------------------------------------------------------------------------
Usage : perl GREGOR.pl --conf [conf.file]
----------------------------------------------------------------------------------

The following command is a typical command line:

perl GREGOR.pl --conf [conf.file]

Example configuration file can be found in example directory. Users have to modify the configurations before running.

== Configuration File ==
The example configuration file below illustrate how to configure the GREGOR configuration file.

###############################################################################
# CHIPSEQ ENRICHMENT CONFIGURATION FILE
# This configuration file contains run-time configuration of
# CHIP_SEQ ENRICHMENT
###############################################################################
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
###############################################################################
INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt ## e.g. /workingdirectory/example/example.index.snps.rsid.list.txt
BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index ## e.g. /workingdirectory/example/example.bed.file.index
REF_DIR = /workingdirectory/ref/ ## reference directory
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
OUT_DIR = /workingdirectory/example/example.rsid.20130808/ ## e.g. /workingdirectory/example/example.rsid.20130808/
MIN_NEIGHBOR_NUM = 500
BEDFILE_IS_SORTED = True
BATCHTYPE = slurm
BATCHOPTS = --partition=main --time=0:30:0

In the config file, there are several parameters to adjust:

INDEX_SNP_FILE: This file contains a single column of trait-associated input SNPs, without a header. Variants can be listed in rsid or hg19 chr:pos format.

BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.

REF_DIR: Define reference file directory which you download at here.

R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size.

OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".

MIN_NEIGHBOR_NUM: Define the minimum number of control SNPs for each index SNP. Script will find no less than this number around every index SNP. If you make this number of control SNPs very large, the control SNPs will be less closely matched on the three matching properties (distance to nearest gene, frequency and number of SNPs in LD).

BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.

BATCHTYPE: We have three options for this parameter. When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".

BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"

== Results Output ==
The file StatisticSummaryFile.txt in the output directory contains enrichment results with the following information:

[[File:GREGOR Summary 20160201.png]]

Bed_File: The individual datasets used in the enrichment analysis

InBed_Index_SNP: Number of index SNPs or their LD proxies that overlaps regulatory regions in each dataset

Pvalue: P-value calculated assuming a sum of binomial distributions to represent the number of index SNPs (or LD proxies) that overlap a dataset compared to the expectation observed in the matched control sets

*Note: SNPs that cannot be converted from rsID to chr:pos format are listed in the output file rsid.index.snp.txt. SNPs for which there are no LD proxies or no MAF data available are listed in the output file nonannoted.index.snp.txt.

== Testing GREGOR ==
There is an example directory in ~/GREGOR. You can find index SNP file, 3 bed files, bed file index and example config file.
After change your config file, you can run a test.

perl ~/GREGOR/script/GREGOR.pl --conf ~/GREGOR/example/example.conf

After running 2 minutes +/- 1 minutes. You will get result file "StatisticSummaryFile.txt" in your defined output directory.

== Acknowledgements ==
GREGOR is the result of collaborative efforts by Cristen Willer, Jin Chen, Wei Zhou, Ellen Schmidt, He Zhang, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] with any questions.

File:GREGOR Summary 20160201.png

2016-02-01T15:25:49Z

Jchen:

GREGOR

2016-02-01T14:55:27Z

2014-09-16T02:42:57Z

Jchen: /* Basic Usage Example */

Genezoom

2014-09-16T02:41:26Z

Jchen: /* Basic Usage Example */

Genezoom

2014-09-16T02:40:11Z

Jchen:

2013-12-03T21:08:21Z

Jchen: /* Update your copy */

==FallInBed==

'''FallInBed''' is a tool to test for global enrichment of trait-associated variants in experimentally annotated regulatory domains. Because all reference data are hg19, make sure your index SNP list and BED files are also in hg19 version.

== Get FallInBed Source Codes ==

=== Download FallInBed from webpage ===

Through this link [http://www.sph.umich.edu/csg/jich/FallInBed/ FallInBed Download], you can download a copy of FallInBed.

=== Download from GitHub with Git ===
You can create your won git clone(copy) using:

git clone https://github.com/jinchen-umich/FallInBed.git
or
git clone git://github.com/jinchen-umich/FallInBed.git

Either of these two commands creates a directory which called FallInBed in the current directory.

=== Update your copy ===
If you have already gotten your copy, using the following commands to update:
1. cd pathToYourCopy/FallInBed
2. git pull

=== Download From GitHub without Git ===
If there is no git in your system, you still can download from GitHub:
# Latest Code (master branch)
#: via Website
#:# Goto : https://github.com/jinchen-umich/FallInBed
#:# Click on the <code>Download ZIP</code> button on the right side panel.
#: via Command Line
#:: <code>wget https://github.com/jinchen-umich/FallInBed/archive/master.zip</code>

After downloading the file, uncompress (unzip/untar) it. The directory created will be named <code>FallInBed</code>.

== Build FallInBed ==

To build FallInBed, copy the FallInBed package to the directory you want, and then run the following command:

tar xzvf FallInBed.tar.gz

After unzip, you can find 3 directories in "FallInBed" (./example ./lib ./script).

== Download reference files ==

Download the reference files from this link [http://www.sph.umich.edu/csg/jich/FallInBed/ FallInBed Download], then un-package the file

tar xzvf FallInBed.ref.tar.gz

After unzip, you will get 47 reference files in the directory "./ref"

== Basic Usage Example ==

When you run

perl FallInBed.pl

you will get some information about FallInBed

----------------------------------------------------------------------------------
FallInBeds.pl : Functional annotation of trait-associated variants
----------------------------------------------------------------------------------
This program tests for enrichment of an input list of trait-associated index
SNPs ([chr:pos] format or rsID, hg19) in experimentally annotated regulatory
domains (BED files).

Note: the index SNPs should be hg19 version. All maf and LD data are from 1000G
EUR samples! (Release date : May 21, 2011)

Version : 1.1.0

Report Bug(s) : jich[at]umich[dot]edu
----------------------------------------------------------------------------------
Usage : perl FallInBeds.pl --conf [conf.file]
----------------------------------------------------------------------------------

The following command is a typical command line:

perl FallInBed.pl --conf [conf.file]

Example configuration file can be found in example directory. Users have to modify the configurations before running.

== Configuration File ==
The example configuration file below illustrate how to configure the FallInBed configuration file.

###############################################################################
# CHIPSEQ ENRICHMENT CONFIGURATION FILE
# This configuration file contains run-time configuration of
# CHIP_SEQ ENRICHMENT
###############################################################################
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
###############################################################################
INDEX_SNP_FILE = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.index.snps.rsid.list.txt ## e.g. /home/myid/data/FallInBed/example.snp.txt
BED_FILE_INDEX = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.bed.file.index ## e.g. /home/myid/data/FallInBed/bedfiles.index
REF_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/ref/ ## reference directory
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
OUT_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.rsid.20130808/ ## e.g. /home/myid/data/FallInBed/result/
MIN_NEIGHBOR_NUM = 500
BEDFILE_IS_SORTED = True
MOSRUN = mosbatch -E/tmp -i -m2000 -j20,43,122,135,137,138,149,151,153,154,155,156,162,163 sh -c

In the config file, there are several parameters to adjust:

INDEX_SNP_FILE: This file contains a single column of trait-associated input SNPs, without a header. Variants can be listed in rsid or hg19 chr:pos format.

BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.

REF_DIR: Define reference file directory which you download at here.

R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.

OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".

MIN_NEIGHBOR_NUM: Define neighbor number around index SNP. Script will find no less than this number around every index SNP.

BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.

== Results Output ==
The file StatisticSummaryFile.txt in the output directory contains enrichment results with the following information:

Bed_File: The individual datasets used in the enrichment analysis

InBed_Index_SNP: Number of index SNPs or their LD proxies that overlaps regulatory regions in each dataset

Pvalue: P-value calculated assuming a sum of binomial distributions to represent the number of index SNPs (or LD proxies) that overlap a dataset compared to the expectation observed in the matched control sets

*Note: SNPs that cannot be converted from rsID to chr:pos format are listed in the output file rsid.index.snp.txt. SNPs for which there are no LD proxies or no MAF data available are listed in the output file nonannoted.index.snp.txt.

== Testing FallInBed ==
There is an example directory in ~/FallInBed. You can find index SNP file, 3 bed files, bed file index and example config file.
After change your config file, you can run a test.

perl ~/FallInBed/script/FallInBed.pl --conf ~/FallInBed/example/example.conf

After running 2 minutes +/- 1 minutes. You will get result file "StatisticSummaryFile.txt" in your defined output directory.

== Acknowledgements ==
FallInBed is the result of collaborative efforts by Cristen Willer, Jin Chen, Wei Zhou, Ellen Schmidt, He Zhang, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] for any questions.