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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
1.22.0
1.20.0
1.18.0
1.16.0
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Version
1.22.0
License
GPL-3
Maintainer
David Clayton
Last Published
December 19th, 2015
Functions in snpStats (1.22.0)
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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