{
  "_id": "6ac89b7bde46216d5edd46bf",
  "Package": "chopsticks",
  "Title": "The 'snp.matrix' and 'X.snp.matrix' Classes",
  "Version": "1.78.0",
  "Date": "2018-02-05",
  "Author": "Hin-Tak Leung <htl10@users.sourceforge.net>",
  "Description": "Implements classes and methods for large-scale SNP\nassociation studies",
  "Maintainer": "Hin-Tak Leung <htl10@users.sourceforge.net>",
  "License": "GPL-3",
  "URL": "http://outmodedbonsai.sourceforge.net/",
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  "Date/Publication": "2026-04-28 12:35:07 UTC",
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      "class": [
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    {
      "page": "snpMatrix-package",
      "title": "The snp.matrix and X.snp.matrix classes",
      "topics": [
        "snpMatrix-package",
        "snpMatrix"
      ]
    },
    {
      "page": "epsout.ld.snp",
      "title": "Function to write an eps file directly to visualize LD",
      "topics": [
        "epsout.ld.snp"
      ]
    },
    {
      "page": "for.exercise",
      "title": "Data for exercise in use of the snpMatrix package",
      "topics": [
        "for.exercise",
        "snp.support",
        "snps.10",
        "subject.support"
      ]
    },
    {
      "page": "glm.test.control",
      "title": "Set up control object for GLM tests",
      "topics": [
        "glm.test.control"
      ]
    },
    {
      "page": "ibs.stats",
      "title": "function to calculate the identity-by-state stats of a group of samples",
      "topics": [
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      ]
    },
    {
      "page": "ibsCount",
      "title": "Count alleles identical by state",
      "topics": [
        "ibsCount"
      ]
    },
    {
      "page": "ibsDist",
      "title": "Distance matrix based on identity by state (IBS)",
      "topics": [
        "ibsDist"
      ]
    },
    {
      "page": "ld.snp",
      "title": "Function to calculate pairwise D', $r^2$",
      "topics": [
        "ld.snp"
      ]
    },
    {
      "page": "ld.with",
      "title": "function to calculate the LD measures of specific SNPs against other SNPs",
      "topics": [
        "ld.with",
        "ld.with,snp.matrix,character-method"
      ]
    },
    {
      "page": "pair.result.ld.snp",
      "title": "Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs",
      "topics": [
        "pair.result.ld.snp"
      ]
    },
    {
      "page": "plot.snp.dprime",
      "title": "Function to draw the pairwise D' in a eps file",
      "topics": [
        "plot.snp.dprime"
      ]
    },
    {
      "page": "qq.chisq",
      "title": "Quantile-quantile plot for chi-squared tests",
      "topics": [
        "qq.chisq"
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    },
    {
      "page": "read.HapMap.data",
      "title": "function to import HapMap genotype data as snp.matrix",
      "topics": [
        "read.HapMap.data"
      ]
    },
    {
      "page": "read.pedfile.info",
      "title": "function to read the accompanying info file of a LINKAGE ped file",
      "topics": [
        "read.pedfile.info"
      ]
    },
    {
      "page": "read.pedfile.map",
      "title": "function to read the accompanying map file of a LINKAGE ped file",
      "topics": [
        "read.pedfile.map"
      ]
    },
    {
      "page": "read.snps.chiamo",
      "title": "Read genotype data from the output of Chiamo",
      "topics": [
        "read.snps.chiamo"
      ]
    },
    {
      "page": "read.snps.long",
      "title": "Read SNP data in long format",
      "topics": [
        "read.snps.long"
      ]
    },
    {
      "page": "read.snps.long.old",
      "title": "Read SNP input data in \"long\" format (old version)",
      "topics": [
        "read.snps.long.old"
      ]
    },
    {
      "page": "read.snps.pedfile",
      "title": "Read genotype data from a LINKAGE \"pedfile\"",
      "topics": [
        "read.snps.pedfile"
      ]
    },
    {
      "page": "read.wtccc.signals",
      "title": "read normalized signals in the WTCCC signal file format",
      "topics": [
        "read.wtccc.signals"
      ]
    },
    {
      "page": "row.summary",
      "title": "Summarize rows of a snp matrix",
      "topics": [
        "row.summary"
      ]
    },
    {
      "page": "single.snp.tests",
      "title": "1-df and 2-df tests for genetic associations with SNPs",
      "topics": [
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    },
    {
      "page": "snp-class",
      "title": "Class \"snp\"",
      "topics": [
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        "coerce,snp,genotype-method",
        "coerce,snp,numeric-method",
        "show,snp-method",
        "snp-class"
      ]
    },
    {
      "page": "snp.cbind",
      "title": "Bind together two or more snp.matrix objects",
      "topics": [
        "cbind",
        "cbind2",
        "rbind",
        "rbind2",
        "snp.cbind",
        "snp.rbind"
      ]
    },
    {
      "page": "snp.cor",
      "title": "Correlations with columns of a snp.matrix",
      "topics": [
        "snp.cor"
      ]
    },
    {
      "page": "snp.dprime-class",
      "title": "Class \"snp.dprime\" for Results of LD calculation",
      "topics": [
        "niceprint",
        "print.snp.dprime",
        "snp.dprime-class"
      ]
    },
    {
      "page": "snp.lhs.tests",
      "title": "Score tests with SNP genotypes as dependent variable",
      "topics": [
        "snp.lhs.tests"
      ]
    },
    {
      "page": "snp.matrix-class",
      "title": "Class \"snp.matrix\"",
      "topics": [
        "cbind,snp.matrix-method",
        "cbind2,snp.matrix,snp.matrix-method",
        "coerce,matrix,snp.matrix-method",
        "coerce,snp.matrix,character-method",
        "coerce,snp.matrix,numeric-method",
        "initialize,snp.matrix-method",
        "is.na,snp.matrix-method",
        "rbind,snp.matrix-method",
        "rbind2,snp.matrix,snp.matrix-method",
        "show,snp.matrix-method",
        "snp.matrix-class",
        "summary,snp.matrix-method",
        "[,snp.matrix,ANY,ANY,ANY-method",
        "[,snp.matrix-method",
        "[,X.snp.matrix,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "snp.pre",
      "title": "Pre- or post-multiply a snp.matrix object by a general matrix",
      "topics": [
        "snp.post",
        "snp.pre"
      ]
    },
    {
      "page": "snp.rhs.tests",
      "title": "Score tests with SNP genotypes as independent variable",
      "topics": [
        "snp.rhs.tests"
      ]
    },
    {
      "page": "snpMatrix-internal",
      "title": "snpMatrix-internal",
      "topics": [
        "convert.snpMatrix",
        "convert.snpMatrix.dir",
        "genotype-class",
        "haplotype-class"
      ]
    },
    {
      "page": "testdata",
      "title": "Test data for the snpMatrix package",
      "topics": [
        "Asnps",
        "Autosomes",
        "subject.data",
        "testdata",
        "Xchromosome",
        "Xsnps"
      ]
    },
    {
      "page": "write.snp.matrix",
      "title": "Write a snp.matrix object as a text file",
      "topics": [
        "write.snp.matrix"
      ]
    },
    {
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