FastQTL

[…] were used in normalization. the cis region was defined as ±1 mb from the transcription start site for each gene. the associations between genotypes and gene quantification were obtained using the fastqtl software., a reduced genome was generated by extracting the sequences flanking the nlaiii restriction sites (30 bp on each strand from the nlaiii restriction sites to downstream) using […]

[…] in the cis-eqtl data by the gtex consortium (n = 277) for subcutaneous adipose tissue, filtered using their permutation test for significance, which used the adaptive permutation scheme in fastqtl and a permutation test p-value threshold equal to the empirical p-value of the gene closest to the fdr 5% threshold, as reported by gtex. only replicated adipose cis-eqtls and their target […]

[…] probes, 423 604 methylation probes, and 8 639 940 genotyped and imputed snps. snp and probes separated by <500 kb were tested for associationbeta distribution-adjusted empirical p-values from fastqtl were used to calculate q-values and a false-discovery rate (fdr) threshold of 0.01 was applied to identify eprobes/mecpgs with a significant eqtl/meqtla counts include snps in high ldb […]

[…] none of the index snps were associated with the expression of their flanking genes, snps in weak ld with rs12302097 were found to be nominally associated with the expression of chst11 (rs56372209, p fastqtl = 0.041, r 2 = 0.3) and txnrd1 (rs73183724, p fastqtl = 0.031, r 2 = 0.25, supplementary data ). using gtex we also found that several snps in complete ld with rs410155 including rs381706 […]

[…] metrics. in addition, we have observed that little, if any, genetic signal is present in the peer factors ()., within each tissue, cis-eqtls were identified by linear regression, as implemented in fastqtl, adjusting for peer factors, sex, genotyping platform, and three genotype-based principal components (pcs). we restricted our search to variants within 1 mb of the tss of each gene and, […]

[…] finally, nominal p-values pnom were transformed to permutation p-values by pperm = p(x > −log10(pnom)) where x ~ g(μ, β). this procedure is conceptually very similar to the one implemented in the fastqtl tool, where beta distribution is used to model the smallest non-transformed p-values []., second, to control for the number of genes tested, we used the bonferroni method. all snp and gene […]