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1. cd pathToYourCopy/FallInBed
1. cd pathToYourCopy/FallInBed
2. git pull
2. git pull
== Build FallInBed ==
== Build FallInBed ==
tar xzvf FallInBed.ref.tar.gz
tar xzvf FallInBed.ref.tar.gz
After unzip, copy all reference files to directory "./ref"
After unzip, you will get 47 reference files in the directory "./ref"
== Basic Usage Example ==
== Basic Usage Example ==
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
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
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
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
LDWINDOWSIZE = 1000000
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.
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.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.
