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### Apply hierarchical multiple testing correction
###
### @param cis_assocs data.table of cis-associations from MatrixEQTL
### @param local multiple testing correction method to use at each gene.
### @param global multiple testing correction method to us across all genes.
### @param tests_per_gene a data.table providing the number of cis SNPs /
### independent tests for each gene.
###
### @return a data.table containing only significant eGenes or significant
### eSNPs
hierarchical_correction <- function(cis_assocs, local, global, tests_per_gene=NULL) {
# Suppress CRAN notes about data.table columns
local_pval <- NULL
pvalue <- NULL
n_tests <- NULL
gene <- NULL
statistic <- NULL
global_pval <- NULL
# Apply local correction across SNPs at each gene
if (!is.null(tests_per_gene)) { # i.e. Bonferroni when test only performed on some SNPs
cis_assocs <- merge(cis_assocs, tests_per_gene, by="gene")
cis_assocs[, local_pval := adjust_p(pvalue, method=local, N=unique(n_tests)), by=gene]
} else {
cis_assocs[, local_pval := adjust_p(pvalue, method=local), by=gene]
}
# Apply global correction across genes using the best p-value per gene
cis_assocs <- cis_assocs[order(abs(statistic), decreasing=TRUE)]
top_assocs <- cis_assocs[, .SD[which.min(local_pval)], by="gene"]
top_assocs[,global_pval := adjust_p(local_pval, method=global)]
cis_assocs <- merge(cis_assocs, top_assocs[,list(gene, global_pval)], by="gene")
return(cis_assocs)
}
### Adjust p-values for multiple tests
adjust_p <- function(pvals, method, N=NULL) {
if (method == "qvalue") {
qvalue::qvalue(pvals)$qvalues
} else if (method == "eigenMT") {
pmin(pvals * N, 1)
} else {
p.adjust(pvals, method, n=ifelse(is.null(N), length(pvals), N))
}
}
### Determine the eSNP significance threshold after hiearchical correction
###
### @param cis_assocs a table of hierarchically corrected associations
get_eSNP_threshold <- function(cis_assocs) {
# Suppress CRAN NOTES
statistic <- NULL
local_pval <- NULL
global_pval <- NULL
# What is the locally corrected p-value corresponding to the global
# correction threshold of 0.05?
cis_assocs <- cis_assocs[order(abs(statistic), decreasing=TRUE)]
top_assocs <- cis_assocs[, .SD[which.min(local_pval)], by="gene"]
top_assocs <- top_assocs[order(global_pval)]
n_sig <- top_assocs[,sum(global_pval < 0.05)]
eSNP_threshold <- top_assocs[n_sig:(n_sig+1), mean(local_pval)]
return(eSNP_threshold)
}
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