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snpStats

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 (55)

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

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

Unpack posterior probabilities from one-byte codes

qq.chisq

Quantile-quantile plot for chi-squared tests

random.snps

Generate random SnpMatrix

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

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.plink

Write files for analysis in the PLINK toolset

write.snp.matrix

Write a SnpMatrix object as a text file

xxt

X.X-transpose for a standardized SnpMatrix

snpStats

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08

snpStats

Functions (55)

snpStats

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