Matrix eQTL protocols

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Matrix eQTL specifications

Information


Unique identifier OMICS_04606
Name Matrix eQTL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.1.0
Stability Stable
Maintained Yes

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Publication for Matrix eQTL

Matrix eQTL in pipelines

 (2)
2016
PMCID: 4807760
PMID: 27015273
DOI: 10.1371/journal.pone.0152425

[…] for each gene. before eqtl analysis, expression quantifications were normalized by peer correction [] and transformed into standard normal distribution. eqtls were mapped using a linear model in matrix eqtl [] and permutations were used for fdr estimation., for fcγr genes with updated refseq annotation, the number of reads uniquely mapped to each gene in each sample was counted using htseq […]

2016
PMCID: 5094714
PMID: 27812116
DOI: 10.1371/journal.pgen.1006407

[…] analysis. for each polymorphic position, the samples were divided into groups according to their allele assignment. as described in lappalainen [] et al., using the linear model implemented in the matrix eqtl r package [], eqtl mapping was calculated according to the allele assignment, while considering gender, mtdna copy number and sample resource (i.e. lab of origin) as covariates. […]


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Matrix eQTL in publications

 (80)
PMCID: 5923247
PMID: 29703885
DOI: 10.1038/s41467-018-03402-w

[…] read term catalog. a final step reduces the number of read terms by collapsing terms with a similar start position and exon content to an approximate target number of read terms of 2500., we used matrix eqtl to perform association mapping for local eqtls and transcript ratio qtls (cis-trqtls), where the ratio of expression levels for each isoform to all isoforms in a gene—or the transcript […]

PMCID: 5904126
PMID: 29666375
DOI: 10.1038/s41398-018-0130-x

[…] association analysis according to individual snp-based analysis, namely rs1948, rs3743075, and rs7178270. they were all intronic polymorphisms associated with the extent of methylation. we used the matrix eqtl (v. 2.1.1) r package to test association of the three snps, with linear regression under an additive model and adjusted for age, smoking status, and whether the subject was a coal miner. […]

PMCID: 5904163
PMID: 29666371
DOI: 10.1038/s41467-018-03554-9

[…] snps. imputed data were filtered using the quality control inclusion criteria of info ≥0.8, maf ≥5%, and hardy–weinberg equilibrium (hwe) p > 0.00001. the cis-eqtl analysis was performed using matrix-eqtl. we classified the variants as in cis if they were within 1 mb of either end of a gene. the first three genetic principal components were included as covariates in the cis-eqtl analysis […]

PMCID: 5897392
PMID: 29650998
DOI: 10.1038/s41598-018-24219-z

[…] we extracted publicly available data and computed the largest eqtl data set for liver tissue to date. genotypes and expression data from all studies underwent rigorous quality control. subsequently, matrix eqtl was used to identify significant local eqtl. in total, liver samples from 588 individuals revealed 202,489 significant eqtl variants affecting 1,959 genes (q-value < 0.001). […]

PMCID: 5840407
PMID: 29511167
DOI: 10.1038/s41467-018-03260-6

[…] and gene expression qcs were considered for eqtl analysis, leaving a sample size of 233. eqtls were identified by using linear regression model and additive genotype effects as implemented in the matrix eqtl package in r. cis-eqtls were defined by a 2 mb window, i.e., 1 mb distance on either side of the snp. eqtls were calculated on adjusted expression traits to obtain test statistics, p […]


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Matrix eQTL institution(s)
Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

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