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snpStats (version 1.18.0)

SnpMatrix and XSnpMatrix classes and methods

Description

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

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Version

Version

1.18.0

License

GPL-3

Maintainer

David Clayton

Last Published

February 15th, 2017

Functions in snpStats (1.18.0)

filter.rules

Filter a set of imputation rules
glm.test.control

Set up control object for GLM computations
Fst

Calculate fixation indices
example-new

An example of intensity data for SNP genotyping
GlmTests-class

Classes "GlmTests" and "GlmTestsScore"
chi.squared

Extract test statistics and p-values
convert.snpMatrix

Convert snpMatrix objects to snpStats objects
families

Test data for family association tests
GlmEstimates-class

Class "GlmEstimates"
for.exercise

Data for exercise in use of the snpStats package
ibsDist

Distance matrix based on identity by state (IBS)
ibsCount

Count alleles identical by state
misinherits

Find non-Mendelian inheritances in family data
mvtests

Multivariate SNP tests
imputation.maf

Extract statistics from imputation rules
ld

Pairwise linkage disequilibrium measures
mean2g

Raw coding of posterior probabilities of SNP genotype
ld.example

Datasets to illustrate calculation of linkage disequilibrium statistics
ImputationRules-class

Class "ImputationRules"
impute.snps

Impute snps
sm.compare

Compare two SnpMatrix objects
qq.chisq

Quantile-quantile plot for chi-squared tests
SnpMatrix-class

Class "SnpMatrix"
read.beagle

Read genotypes imputed by the BEAGLE program
snpStats-package

SnpMatrix and XSnpMatrix classes and methods
pool2

Pool results of tests from two independent datasets
snp.cor

Correlations with columns of a SnpMatrix
SingleSnpTests-class

Classes "SingleSnpTests" and "SingleSnpTestsScore"
single.snp.tests

1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs)
pp

Unpack posterior probabilities from one-byte codes
read.plink

Read a PLINK binary data file as a SnpMatrix
read.snps.long

Read SNP data in long format (deprecated)
pool

Pool test results from several studies or sub-studies
testdata

Test data for the snpStats package
test.allele.switch

Test for switch of alleles between two collections
plotUncertainty

Plot posterior probabilities of genotype assignment
tdt.snp

1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) in family data
XSnpMatrix-class

Class "XSnpMatrix"
switch.alleles

Switch alleles in columns of a SnpMatrix or in test results
xxt

X.X-transpose for a standardized SnpMatrix
write.plink

Write files for analysis in the PLINK toolset
write.SnpMatrix

Write a SnpMatrix object as a text file
row.summary

Summarize rows or columns of a snp matrix
read.mach

Read genotypes imputed by the MACH program
sample.ped.gz

Sample datasets to illustrate data input
read.pedfile

Read a pedfile as "SnpMatrix" object
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
read.long

Read SNP genotype data in long format
read.impute

Read genotypes imputed by the IMPUTE2 program
snp.imputation

Calculate imputation rules
snp.rhs.tests

Score tests with SNP genotypes as independent variable
snp.lhs.estimates

Logistic regression with SNP genotypes as dependent variable
snp.rhs.estimates

Fit GLMs with SNP genotypes as independent variable(s)