You can install lassosum and its dependencies in R with the following command: Again, we assume that we have the following files (or you can download it from here): # Prefer to work with data.table as it speeds up file reading, # For multi-threading, you can use the parallel package and, # invoke cl which is then passed to lassosum.pipeline, # Need as.data.frame here as lassosum doesn't handle data.table, # We will need the EUR.hg19 file provided by lassosum. This tutorial only uses fake data for educational purposes. For more details, please refer to lassosum's homepage. max AUC). For more information, please refer to this paper, "https://github.com/privefl/bigsnpr/raw/master/data-raw/hm3_variants.rds", # LDpred 2 require the header to follow the exact naming, # Initialize variables for storing the LD score and LD matrix, # We want to know the ordering of samples in the bed file, # preprocess the bed file (only need to do once for each data set), # extract the SNP information from the genotype, # Assign the genotype to a variable for easier downstream analysis, # get the CM information from 1000 Genome, # will download the 1000G file to the current directory (". These 4 variables are used to match variants between the two data frames. First, you need to read genotype data from the PLINK files (or BGEN files) as well as the text file containing summary statistics. length.out = 30). First, you need to compute correlations between variants. "), # Extract SNPs that are included in the chromosome, # We assume the fam order is the same across different chromosomes, # Assuming the file naming is EUR_chr#.bed, # Reformat the phenotype file such that y is of the same order as the, # (will also need the fmsb package to calculate the pseudo R2), Basic Tutorial for Polygenic Risk Score Analyses, 1. You can find the accompany tutorial here PRSice-2: Polygenic Risk Score software PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. However, in many cases, the ordering of the summary statistics differ, The script used here is based on LDpred 2 implemented under bigsnpr version 1.4.7. In practice, we recommend to test multiple values for h2 and p. You can then choose the best model according to your preferred criterion (e.g. The script used here is based on LDpred 2 implemented under bigsnpr version 1.4.7, For more details, please refer to LDpred 2's homepage. Get the final performance of the LDpred models, The genotype file after performing some basic filtering, This file contains the SNPs that passed the basic filtering, This file contains the samples that passed the basic filtering, This file contains the phenotype of the samples, This file contains the covariates of the samples, This file contains the PCs of the samples. # Remove P-value = 0, which causes problem in the transformation, # Transform the P-values into correlation, # The cluster parameter is used for multi-threading, # You can ignore that if you do not wish to perform multi-threaded processing, Basic Tutorial for Polygenic Risk Score Analyses, The genotype file after performing some basic filtering, This file contains the SNPs that passed the basic filtering, This file contains the samples that passed the basic filtering, This file contains the phenotype of the samples, This file contains the covariates of the samples, This file contains the PCs of the samples.
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