Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
|Author||David Clayton <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||David Clayton <email@example.com>|
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
Fst: Calculate fixation indices
GlmEstimates-class: Class "GlmEstimates"
glm.test.control: Set up control object for GLM computations
GlmTests-class: Classes "GlmTests" and "GlmTestsScore"
ibsCount: Count alleles identical by state
ibsDist: Distance matrix based on identity by state (IBS)
imputation.maf: Extract statistics from imputation rules
ImputationRules-class: Class "ImputationRules"
impute.snps: Impute snps
ld: Pairwise linkage disequilibrium measures
ld.example: Datasets to illustrate calculation of linkage disequilibrium...
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
pp: 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...
SingleSnpTests-class: Classes "SingleSnpTests" and "SingleSnpTestsScore"
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
SnpMatrix-class: Class "SnpMatrix"
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...
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
XSnpMatrix-class: Class "XSnpMatrix"
xxt: X.X-transpose for a standardized SnpMatrix