Man pages for snpStats
SnpMatrix and XSnpMatrix classes and methods

chi.squaredExtract test statistics and p-values
convert.snpMatrixConvert 'snpMatrix' objects to 'snpStats' objects
example-newAn example of intensity data for SNP genotyping
familiesTest data for family association tests
filter.rulesFilter a set of imputation rules
for.exerciseData for exercise in use of the snpStats package
FstCalculate fixation indices
GlmEstimates-classClass "GlmEstimates"
glm.test.controlSet up control object for GLM computations
GlmTests-classClasses "GlmTests" and "GlmTestsScore"
ibsCountCount alleles identical by state
ibsDistDistance matrix based on identity by state (IBS)
imputation.mafExtract statistics from imputation rules
ImputationRules-classClass "ImputationRules"
impute.snpsImpute snps
ldPairwise linkage disequilibrium measures
ld.exampleDatasets to illustrate calculation of linkage disequilibrium...
mean2gRaw coding of posterior probabilities of SNP genotype
misinheritsFind non-Mendelian inheritances in family data
mvtestsMultivariate SNP tests
plotUncertaintyPlot posterior probabilities of genotype assignment
poolPool test results from several studies or sub-studies
pool2Pool results of tests from two independent datasets
ppUnpack posterior probabilities from one-byte codes
qq.chisqQuantile-quantile plot for chi-squared tests
random.snpsGenerate random SnpMatrix
read.beagleRead genotypes imputed by the BEAGLE program
read.imputeRead genotypes imputed by the IMPUTE2 program
read.longRead SNP genotype data in long format
read.machRead genotypes imputed by the MACH program
read.pedfileRead a pedfile as '"SnpMatrix"' object
read.plinkRead a PLINK binary data file as a SnpMatrix
read.snps.longRead SNP data in long format (deprecated)
row.summarySummarize rows or columns of a snp matrix
sampleSample datasets to illustrate data input
single.snp.tests1-df and 2-df tests for genetic associations with SNPs (or...
SingleSnpTests-classClasses "SingleSnpTests" and "SingleSnpTestsScore"
sm.compareCompare two SnpMatrix objects
snp.corCorrelations with columns of a SnpMatrix
snp.imputationCalculate imputation rules
snp.lhs.estimatesLogistic regression with SNP genotypes as dependent variable
snp.lhs.testsScore tests with SNP genotypes as dependent variable
SnpMatrix-classClass "SnpMatrix"
snp.pre.multiplyPre- or post-multiply a SnpMatrix object by a general matrix
snp.rhs.estimatesFit GLMs with SNP genotypes as independent variable(s)
snp.rhs.testsScore tests with SNP genotypes as independent variable
snpStats-packageSnpMatrix and XSnpMatrix classes and methods
switch.allelesSwitch alleles in columns of a SnpMatrix or in test results
tdt.snp1-df and 2-df tests for genetic associations with SNPs (or...
test.allele.switchTest for switch of alleles between two collections
testdataTest data for the snpStats package
write.plinkWrite files for analysis in the PLINK toolset
write.snp.matrixWrite a SnpMatrix object as a text file
XSnpMatrix-classClass "XSnpMatrix"
xxtX.X-transpose for a standardized SnpMatrix
snpStats documentation built on Nov. 17, 2017, 9:07 a.m.