===================== INSTRUCTIONS ============================== This document contains instructions for installing and using the LBL package for R. 1. Install For Linux users, download the compiled R package file: LBL_1.0.tar.gz Then use the following function in R to install the package >install.packages(pkgs=filename,repos=NULL) where "filename" should be replaced with the corresponding file name (LBL_1.0.tar.gz) with the correct path. Alternatively, at the Linux command line, you may type "R CMD INSTALL PACKAGE_DIRECTORY/LBL_1.0.tar.gz" where PACKAGE_DIRECTORY is the folder containing LBL_1.0.tar.gz. You also need to install the hapassoc package: >install.packages(pkgs="hapassoc") 2. Usage #Load the packages into R >library(LBL) >library(hapassoc) #Read the details about the package >?LBL #Rad the details about the function and an example for runing the function. >?BL 3. Example Using the example data file: LBL.ex #load the example dataset that is included in the package > data(LBL.ex) #run hapassoc to get initial alleles frequencies and learn about the possible haplotypes for each individual from SNP data > set.seed(12) > hapassoc.out<-pre.hapassoc(LBL.ex, 5, pooling.tol=0) #Run BL to make inference on association of haplotypes with the disease. #Note: The defaul setting are burn.in = 20000, num.it = 50000 in the BL function. However, for a quick check to make sure that the package is loaded properly, the example uses much smaller numbers. > out.BL<-BL(hapassoc.out, burn.in=100, num.it=1000) #Note that results indicate that one rare haplotype (h10100) and one common haplotype (h1111) are associated with the disease (CI of OR deosn't include 1) and BF is large > ans <- cbind(out.BL$CI.freq[1:5,1],out.BL$freq[1:5],out.BL$CI.freq[1:5,2:3],out.BL$OR,out.BL$CI.OR[,2:3],out.BL$BF) > names(ans) <- c("Hap","Freq", "Lower", "Upper", "OR", "Lower", "Upper", "BF") > ans Hap Freq Lower Upper OR Lower Upper 1 h01100 0.307104893 0.286350143 0.336621845 0.9142706 0.7646977 1.074237 2 h10100 0.003168834 0.001454167 0.005474429 3.8391766 1.6669506 10.167419 3 h11011 0.010171629 0.005514717 0.015907211 0.8704939 0.3614772 1.680056 4 h11100 0.168755504 0.148870042 0.189348930 0.8761900 0.6807242 1.113297 5 h11111 0.098177629 0.079741332 0.112352341 1.8405174 1.3549340 2.557672 BF 1 0.07877372 2 31.36377758 3 0.33832517 4 0.18558448 5 >100 4. References Biswas S, and Lin, S. (2011) Logistic Bayesian Lasso for identifying association with rare haplotypes and application to age-related macular degeneration. Manuscript. Burkett K, Graham J and McNeney B (2006). hapassoc: Software for Likelihood Inference of Trait Associations with SNP Haplotypes and Other Attributes. Journal of Statistical Software, *16(2)*:1-19 ----------------------------------------------------------------- If you have any questions, please email Swati Biswas at Swati.Biswas@unthsc.edu or Shili Lin at shili@stat.osu.edu