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R2THRESHOLD = 0.7
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
LDWINDOWSIZE = 1000000
RANDOM_LIST_NUM = 1000
OUT_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.rsid.20130808/ ## e.g. /home/myid/data/FallInBed/result/
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
MIN_NEIGHBOR_NUM = 500
In configure file, there are 10 parameters.
In the configure file, there are 8 parameters to adjust:
INDEX_SNP_FILE: define the index SNP file. In this file, there is only one column without header. Index SNP can be rsid or chr/pos format.
INDEX_SNP_FILE: This file lists the trait-associated input SNPs for enrichment analysis. In this file, there is a single column without a header. Index SNPs can be in rsid or chr:pos format.
BED_FILE_INDEX: define the bed files.
BED_FILE_INDEX: This is a file listing the BED files with complete paths to their locations to be used for enrichment analysis.
R2THRESHOLD and LDWINDOWSIZE: these two parameters are defined the LD buddy.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.
RANDOM_LIST_NUM: define how many random lists, e.g. 100 or 1000
RANDOM_LIST_NUM: Define how many random lists, e.g. 100 or 1000
OUT_DIR: All result files are saved to this folder. In this folder, script will create multi-subdirectories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
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.
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.
== Acknowledgements ==
== Acknowledgements ==
FallInBed is a result from collaborative effort by Cristen Willer, Jin Chen, Wei Zhou, Ellen Marie Schmidt, He Zhang, and Goncalo Abecasis. Please email to Cristen Willer [cristen@umich.edu ] for any questions.
FallInBed is a result from 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.
