snpStats v1.22.0

by David Clayton

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
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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

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