vignettes/GWAS_with_mtmcskat.md

In naglemi/mtmcskat: Multi-Threaded Monte Carlo Sequence Kernel Association Test (MTMC-SKAT)

GWAS workflows with MTMC-SKAT

In this vignette, we describe key mid-level functions provided by the MTMC-SKAT package, their usage in the standard automated workflow and how they can be used to produce a custom workflow.

# library(SKATMCMT)

Initial analysis prior to resampling

Preparation of SNP data for analysis

The function pre_allocate is used to load SNP data from the .traw format and convert it to a list of SNP windows. The resulting list is saved in the directory specified by pre_allocated_dir. To avoid regenerating a list used for multiple analyses, pre_allocate will read in the corresponding list for a genotype file if one exists.

pre_allocated_SNP_windows <- pre_allocate(raw_file_path = "poplar_Chr10_portion.traw",
                                          window_size = 3000,
                                          window_shift = 1000,
                                          pre_allocated_dir = "pre_allocated/")

Multi-threaded SKAT

Upon pre-allocating SNP window data, we can begin the initial round of SKAT, without resampling, to produce inital p-values for each SNP window without any permutations. From these initial results, the user or preprogrammed filters can select SNP windows deemed interesting and perform MTMC-SKAT to calculate empirical p-values for these SNP windows. The provided function for multi-threaded SKAT (mtskat) runs SKAT over pre-allocated SNP windows, with chunks of SNP windows distributed among cores.

results_sans_resampling <- mtskat(pre_allocated_SNP_windows = pre_allocated_SNP_windows
                                  phenotype = read.csv("poplar_shoot_sample.csv"),
                                  covariates = read.csv("poplar_PC_covariates.csv"),
                                  ncore = "AllCores")

Calculation of empirical p-values for selected SNP windows

Selection of SNP windows

Based on initial results, batches of SNP windows producing p-values over a given range of interest can be selected using extract_windows_range_p. As in the standard automated workflow, we recommend the range of p-values for each batch of SNPs vary by no more than an order of magnitude, to allow calculation of empirical p-values to a desired accuracy without an unnecesary number of permutations.

window_list <- extract_windows_range_p(data = results_sans_resampling,
                                       upper_bound = 10^-2,
                                       lower_bound = 10^-3)
new_pre_allocated_SNP_windows <- subset_list_of_lists(list_of_lists = pre_allocated_SNP_windows,
                                                      desired_list = window_list)

Multi-threaded Monte Carlo SKAT

Once this subset of SNP windows has been pre-allocated into a new list, empirical p-values can be calculated using mtmcskat with the multithreading option set to snp (to parallelize over SNP windows) or nm (to parallelize over permuted null models). The former is more efficient when 1) a sufficient number of permuted null models for the desired accuracy of empirical p-values can be stored in memory; and 2) The number of SNP windows is no less than the number of cores. For lower p-value ranges requiring larger number of permutations and with smaller batches of SNP windows, the latter mode becomes more efficient. In the standard automated workflow, the appropriate function is used for each batch of SNPs based on these criteria.

batch_results_with_resampling_over_SNPs <- mtmcskat(pre_allocated_SNP_windows = new_pre_allocated_SNP_windows,
                                                    phenotype = read.csv("poplar_shoot_sample.csv"),
                                                    covariates = read.csv("poplar_PC_covariates.csv"),
                                                    ncore = "AllCores",
                                                    multithreading = "snp")

batch_results_with_resampling_over_NMs <- mtmcskat(pre_allocated_SNP_windows = new_pre_allocated_SNP_windows,
                                                    phenotype = read.csv("poplar_shoot_sample.csv"),
                                                    covariates = read.csv("poplar_PC_covariates.csv"),
                                                    ncore = "AllCores",
                                                    multithreading = "nm")

Re-testing of selected SNP windows

In rare cases, empirical p-values may be significantly lower than initial p-values, leading to fewer significant figures for an empirical p-value than expected given the number of permutations run. These SNP windows can then be extracted for subsequent rounds of analyses with more permutations, until the desired number of significant figures or accuracy limit is reached.

window_list <- extract_windows_sig_fig(data = batch_results_with_resampling_over_NMs,
                                       n_sig_fig = 1) # Suppose we desire two significant figures and thus want all windows for which empirical p-values only have one
new_pre_allocated_SNP_windows <- subset_list_of_lists(list_of_lists = pre_allocated_SNP_windows,
                                                      desired_list = window_list)

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naglemi/mtmcskat documentation built on Aug. 23, 2023, 5:35 p.m.