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  "Package": "MatrixEQTL",
  "Type": "Package",
  "Title": "Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix\nOperations",
  "Version": "2.3",
  "Date": "2019-12-04",
  "Authors@R": "person(  \"Andrey A\", \"Shabalin\",\nrole = c(\"aut\", \"cre\"),\nemail = \"andrey.shabalin@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0309-6821\"))",
  "Description": "Matrix eQTL is designed for fast eQTL analysis on large\ndatasets. Matrix eQTL can test for association between genotype\nand gene expression using linear regression with either\nadditive or ANOVA genotype effects. The models can include\ncovariates to account for factors as population stratification,\ngender, and clinical variables. It also supports models with\nheteroscedastic and/or correlated errors, false discovery rate\nestimation and separate treatment of local (cis) and distant\n(trans) eQTLs. For more details see Shabalin (2012)\n<doi:10.1093/bioinformatics/bts163>.",
  "License": "LGPL-3",
  "LazyLoad": "yes",
  "BugReports": "https://github.com/andreyshabalin/MatrixEQTL/issues",
  "URL": "http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/",
  "Repository": "https://andreyshabalin.r-universe.dev",
  "Date/Publication": "2023-09-26 22:47:34 UTC",
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  "Packaged": {
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    "User": "root"
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  "Author": "Andrey A Shabalin [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0309-6821>)",
  "Maintainer": "Andrey A Shabalin <andrey.shabalin@gmail.com>",
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    "author": "Andrey Shabalin <andrey.shabalin@gmail.com>",
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    "rowSums",
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      "name": "Covariates",
      "title": "Artificial data for Matrix eQTL sample code: Covariates.",
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      "class": [
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      ],
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      "object": "GE",
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      "class": [
        "data.frame"
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        "Sam_02",
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        "Sam_04",
        "Sam_05",
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        "Sam_10",
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        "Sam_13",
        "Sam_14",
        "Sam_15",
        "Sam_16"
      ],
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Artificial data for Matrix eQTL sample code: Gene location file.",
      "object": "geneloc",
      "file": "geneloc.txt.gz",
      "class": [
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      ],
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        "left",
        "right"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "SNP",
      "title": "Artificial data for Matrix eQTL sample code: Genotype.",
      "object": "SNP",
      "file": "SNP.txt.gz",
      "class": [
        "data.frame"
      ],
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        "Sam_01",
        "Sam_02",
        "Sam_03",
        "Sam_04",
        "Sam_05",
        "Sam_06",
        "Sam_07",
        "Sam_08",
        "Sam_09",
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        "Sam_15",
        "Sam_16"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "snpsloc",
      "title": "Artificial data for Matrix eQTL sample code: SNP location file.",
      "object": "snpsloc",
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      "tojson": true
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    {
      "page": "MatrixEQTL-package",
      "title": "Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations",
      "topics": [
        "MatrixEQTL-package",
        "MatrixEQTL"
      ]
    },
    {
      "page": "Covariates",
      "title": "Artificial data for Matrix eQTL sample code: Covariates.",
      "topics": [
        "Covariates"
      ]
    },
    {
      "page": "GE",
      "title": "Artificial data for Matrix eQTL sample code: Gene expression.",
      "topics": [
        "GE"
      ]
    },
    {
      "page": "geneloc",
      "title": "Artificial data for Matrix eQTL sample code: Gene location file.",
      "topics": [
        "geneloc"
      ]
    },
    {
      "page": "Matrix_eQTL_main",
      "title": "Main function for fast eQTL analysis in MatrixEQTL package",
      "topics": [
        "Matrix_eQTL_engine",
        "Matrix_eQTL_main"
      ]
    },
    {
      "page": "MatrixEQTL_cis_code",
      "title": "Sample code for cis/trans-eQTL analysis with Matrix eQTL",
      "topics": [
        "MatrixEQTL_cis_code"
      ]
    },
    {
      "page": "modelANOVA",
      "title": "Constant for 'Matrix_eQTL_engine'.",
      "topics": [
        "modelANOVA"
      ]
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      "topics": [
        "modelLINEAR"
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      "topics": [
        "modelLINEAR_CROSS"
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    },
    {
      "page": "plot.MatrixEQTL",
      "title": "Plot histogram or QQ-plot of all p-values",
      "topics": [
        "plot.MatrixEQTL"
      ]
    },
    {
      "page": "SlicedData-class",
      "title": "Class 'SlicedData' for storing large matrices",
      "topics": [
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        "colMeans,SlicedData-method",
        "colnames,SlicedData-method",
        "colnames<-,SlicedData-method",
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