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rrintcc_read.me
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rrintcc_read.me
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Usage of rrintcc_BOOST
******************************************************************
1. The parameters that can be added in command line
******************************************************************
--config (-c): specify the file that contains filename configuration (default: configNames.txt)
--silent (-s): do not output information
--max-cov: specify the maximum range of the cov matrix (default: 20000: meaning the cov matrix is at most 20000 * 20000)
--all (-a): the set names will be read from the folder setpath, with locipair0.set ~ locipairk.set (k=setnumber-1)
e.g.
./rrintcc_BOOST --config configNames_tmp.txt --silent --max-cov 10000
******************************************************************
2. The format of configNames.txt (below is an example)
******************************************************************
# Formats for configNames.txt
# '#' can be used in the front of a line to comment this line
# Empty lines are permited in this file
# The filenames need not be ordered
# There should be two words per line
# The two words should be separated by spaces or tabs
# The first word in a line is the variable name in rrintcc
# The second word in a line is the content for this variable
# Variables that need to be specified in this file:
# foutpath, resname, logname, filename, mapname, setpath, setname
foutpath Results/snp_results/
resname Results/region_pair_results.txt
logname Results/rrintcc_BOOST.log
filename Data/filenamelist.txt
mapname Data/example_bt_tag.map
setname Data/example_bt_tag.set
# Format of .set/.snps names: locipair1/2/.../.set/snp
setpath all_sets/
******************************************************************
3. The format of filename in configNames.txt (e.g. filenamelist.txt)
******************************************************************
The filename in configNames.txt is consistent with BOOST and GBOOST, should contains the BOOST-formated file that need to be analyzed.
PLINK-formated files (.ped .frq) can be transformed to BOOST-formated using preprocessing_BOOST.py
.bed/.bim/.fam files can be transformed to .ped/.frq using plink1.9, e.g.
plink1.9 --bfile MIGen_QC --recode --out MIGen_QC
.frq file can be generated using plink1.9, e.g.
plink1.9 --file MIGen_QC --freq --out MIGen_QC
plink1.9 --bfile MIGen_QC --freq --out MIGen_QC
******************************************************************
4. Install R, Rcpp and RInside dependencies
******************************************************************
1). Need to install R base env
sudo apt install r-base-core
2). Also Need to install mvtnorm, Rcpp and RInside (The packages can be downloaded online)
sudo R CMD INSTALL xxx.tar.gz