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snpStats (version 1.22.0)

SnpMatrix and XSnpMatrix classes and methods

Description

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

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Version

Version

1.22.0

License

GPL-3

Maintainer

David Clayton

Last Published

February 15th, 2017

Functions in snpStats (1.22.0)

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