# snpStats v1.22.0

## SnpMatrix and XSnpMatrix classes and methods

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

## Functions in snpStats

Name | Description | |

ld.example | Datasets to illustrate calculation of linkage disequilibrium statistics | |

snp.cor | Correlations with columns of a SnpMatrix | |

ibsDist | Distance matrix based on identity by state (IBS) | |

snp.rhs.tests | Score tests with SNP genotypes as independent variable | |

GlmEstimates-class | Class "GlmEstimates" | |

read.mach | Read genotypes imputed by the MACH program | |

mvtests | Multivariate SNP tests | |

tdt.snp | 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) in family data | |

switch.alleles | Switch alleles in columns of a SnpMatrix or in test results | |

convert.snpMatrix | Convert snpMatrix objects to snpStats objects | |

snp.imputation | Calculate imputation rules | |

read.pedfile | Read a pedfile as "SnpMatrix" object | |

xxt | X.X-transpose for a standardized SnpMatrix | |

GlmTests-class | Classes "GlmTests" and "GlmTestsScore" | |

chi.squared | Extract test statistics and p-values | |

testdata | Test data for the snpStats package | |

glm.test.control | Set up control object for GLM computations | |

pool2 | Pool results of tests from two independent datasets | |

read.plink | Read a PLINK binary data file as a SnpMatrix | |

snp.pre.multiply | Pre- or post-multiply a SnpMatrix object by a general matrix | |

misinherits | Find non-Mendelian inheritances in family data | |

snpStats-package | \Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}snpStatsSnpMatrix and XSnpMatrix classes and methods | |

write.SnpMatrix | Write a SnpMatrix object as a text file | |

read.long | Read SNP genotype data in long format | |

snp.lhs.tests | Score tests with SNP genotypes as dependent variable | |

read.snps.long | Read SNP data in long format (deprecated) | |

test.allele.switch | Test for switch of alleles between two collections | |

row.summary | Summarize rows or columns of a snp matrix | |

imputation.maf | Extract statistics from imputation rules | |

read.beagle | Read genotypes imputed by the BEAGLE program | |

sm.compare | Compare two SnpMatrix objects | |

sample.ped.gz | Sample datasets to illustrate data input | |

pool | Pool test results from several studies or sub-studies | |

SnpMatrix-class | Class "SnpMatrix" | |

for.exercise | Data for exercise in use of the snpStats package | |

plotUncertainty | Plot posterior probabilities of genotype assignment | |

ImputationRules-class | Class "ImputationRules" | |

example-new | An example of intensity data for SNP genotyping | |

filter.rules | Filter a set of imputation rules | |

ld | Pairwise linkage disequilibrium measures | |

qq.chisq | Quantile-quantile plot for chi-squared tests | |

pp | Unpack posterior probabilities from one-byte codes | |

snp.lhs.estimates | Logistic regression with SNP genotypes as dependent variable | |

random.snps | Generate random SnpMatrix | |

families | Test data for family association tests | |

SingleSnpTests-class | Classes "SingleSnpTests" and "SingleSnpTestsScore" | |

mean2g | Raw coding of posterior probabilities of SNP genotype | |

write.plink | Write files for analysis in the PLINK toolset | |

XSnpMatrix-class | Class "XSnpMatrix" | |

ibsCount | Count alleles identical by state | |

single.snp.tests | 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) | |

impute.snps | Impute snps | |

read.impute | Read genotypes imputed by the IMPUTE2 program | |

snp.rhs.estimates | Fit GLMs with SNP genotypes as independent variable(s) | |

Fst | Calculate fixation indices | |

No Results! |

## Last year downloads

## Details

Date | 2015-12-19 |

License | GPL-3 |

Collate | ss.R contingency.table.R convert.R compare.R glm-test.R imputation.R indata.R long.R misc.R ld.R mvtests.R pedfile.R outdata.R plink.R qc.R qq-chisq.R single.R tdt-single.R structure.R xstuff.R |

LazyLoad | yes |

biocViews | Microarray, SNP, GeneticVariability |

Packaged | 2015-12-19 |

depends | base (>= 2.10.0) , Matrix , methods , survival |

imports | BiocGenerics , graphics , grDevices , stats , utils , zlibbioc |

suggests | hexbin |

Contributors | David Clayton |

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