Classes and statistical methods for large SNP association studies, extending the snpMatrix package

Package: | snpStats |

Version: | 1.15.4 |

Date: | 2014-08-17 |

Depends: | R(>= 2.10.0), survival, Matrix, methods |

Imports: | graphics, grDevices, stats, utils, BiocGenerics, zlibbioc |

Suggests: | hexbin |

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: | 2014-08-17 |

Built: | R 3.1.1; x86_64-pc-linux-gnu; 2014-08-17 12:28:22 UTC; unix |

Index:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | ```
Fst Calculate fixation indices
GlmEstimates-class Class "GlmEstimates"
GlmTests-class Classes "GlmTests" and "GlmTestsScore"
ImputationRules-class Class "ImputationRules"
SingleSnpTests-class Classes "SingleSnpTests" and
"SingleSnpTestsScore"
SnpMatrix-class Class "SnpMatrix"
XSnpMatrix-class Class "XSnpMatrix"
chi.squared Extract test statistics and p-values
convert.snpMatrix Convert 'snpMatrix' objects to 'snpStats'
objects
example-new An example of intensity data for SNP genotyping
families Test data for family association tests
filter.rules Filter a set of imputation rules
for.exercise Data for exercise in use of the snpStats
package
glm.test.control Set up control object for GLM computations
ibsCount Count alleles identical by state
ibsDist Distance matrix based on identity by state
(IBS)
imputation.maf Extract statistics from imputation rules
impute.snps Impute snps
ld Pairwise linkage disequilibrium measures
ld.example Datasets to illustrate calculation of linkage
disequilibrium statistics
mean2g Raw coding of posterior probabilities of SNP
genotype
misinherits Find non-Mendelian inheritances in family data
mvtests Multivariate SNP tests
plotUncertainty Plot posterior probabilities of genotype
assignment
pool Pool test results from several studies or
sub-studies
pool2 Pool results of tests from two independent
datasets
pp Unpack posterior probabilities from one-byte
codes
qq.chisq Quantile-quantile plot for chi-squared tests
read.beagle Read genotypes imputed by the BEAGLE program
read.impute Read genotypes imputed by the IMPUTE2 program
read.long Read SNP genotype data in long format
read.mach Read genotypes imputed by the MACH program
read.pedfile Read a pedfile as '"SnpMatrix"' object
read.plink Read a PLINK binary data file as a SnpMatrix
read.snps.long Read SNP data in long format (deprecated)
row.summary Summarize rows or columns of a snp matrix
sample.info Sample datasets to illustrate data input
single.snp.tests 1-df and 2-df tests for genetic associations
with SNPs (or imputed SNPs)
sm.compare Compare two SnpMatrix objects
snp.cor Correlations with columns of a SnpMatrix
snp.imputation Calculate imputation rules
snp.lhs.estimates Logistic regression with SNP genotypes as
dependent variable
snp.lhs.tests Score tests with SNP genotypes as dependent
variable
snp.pre.multiply Pre- or post-multiply a SnpMatrix object by a
general matrix
snp.rhs.estimates Fit GLMs with SNP genotypes as independent
variable(s)
snp.rhs.tests Score tests with SNP genotypes as independent
variable
snpStats-package SnpMatrix and XSnpMatrix classes and methods
switch.alleles Switch alleles in columns of a SnpMatrix or in
test results
tdt.snp 1-df and 2-df tests for genetic associations
with SNPs (or imputed SNPs) in family data
test.allele.switch Test for switch of alleles between two
collections
testdata Test data for the snpStats package
write.SnpMatrix Write a SnpMatrix object as a text file
write.plink Write files for analysis in the PLINK toolset
xxt X.X-transpose for a standardized SnpMatrix
``` |

David Clayton <[email protected]>

Maintainer: David Clayton <[email protected]>

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