SnpMatrix and XSnpMatrix classes and methods


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Documentation for package ‘snpStats’ version 1.14.0

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A C D E F G I L M N P Q R S T W X Y misc

snpStats-package SnpMatrix and XSnpMatrix classes and methods

-- A --

Asnps Test data for the snpStats package
Autosomes Test data for the snpStats package

-- C --

can.impute Extract statistics from imputation rules
cbind-method Class "SnpMatrix"
cbind2-method Class "SnpMatrix"
ceph.1mb Datasets to illustrate calculation of linkage disequilibrium statistics
chi.squared Extract test statistics and p-values
chi.squared-method Classes "GlmTests" and "GlmTestsScore"
chi.squared-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
coerce-method Class "GlmEstimates"
coerce-method Classes "GlmTests" and "GlmTestsScore"
coerce-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
coerce-method Class "SnpMatrix"
coerce-method Class "XSnpMatrix"
col.summary Summarize rows or columns of a snp matrix
convert.snpMatrix Convert 'snpMatrix' objects to 'snpStats' objects
convert.snpMatrix.dir Convert 'snpMatrix' objects to 'snpStats' objects

-- D --

deg.freedom Extract test statistics and p-values
deg.freedom-method Classes "GlmTests" and "GlmTestsScore"

-- E --

effect.sign Extract test statistics and p-values
effect.sign-method Classes "GlmTests" and "GlmTestsScore"
effect.sign-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
effective.sample.size Extract test statistics and p-values
effective.sample.size-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
example-new An example of intensity data for SNP genotyping

-- F --

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

-- G --

g2post Raw coding of posterior probabilities of SNP genotype
genotypes Test data for family association tests
glm.test.control Set up control object for GLM computations
GlmEstimates-class Class "GlmEstimates"
GlmTests-class Classes "GlmTests" and "GlmTestsScore"
GlmTestsScore-class Classes "GlmTests" and "GlmTestsScore"

-- I --

ibsCount Count alleles identical by state
ibsDist Distance matrix based on identity by state (IBS)
imputation.maf Extract statistics from imputation rules
imputation.nsnp Extract statistics from imputation rules
imputation.r2 Extract statistics from imputation rules
ImputationRules-class Class "ImputationRules"
impute.snps Impute snps
initialize-method Class "SnpMatrix"
initialize-method Class "XSnpMatrix"
is.na-method Class "SnpMatrix"

-- L --

ld Pairwise linkage disequilibrium measures
ld.example Datasets to illustrate calculation of linkage disequilibrium statistics

-- M --

mach1.out.mlprob.gz Sample datasets to illustrate data input
mean2g Raw coding of posterior probabilities of SNP genotype
misinherits Find non-Mendelian inheritances in family data
mvtests Multivariate SNP tests

-- N --

names-method Classes "GlmTests" and "GlmTestsScore"
names-method Classes "SingleSnpTests" and "SingleSnpTestsScore"

-- P --

p.value Extract test statistics and p-values
p.value-method Classes "GlmTests" and "GlmTestsScore"
p.value-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
pedData Test data for family association tests
plot-method Class "ImputationRules"
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
pool2-method Classes "GlmTests" and "GlmTestsScore"
pool2-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
post2g Raw coding of posterior probabilities of SNP genotype
pp Unpack posterior probabilities from one-byte codes

-- Q --

qq.chisq Quantile-quantile plot for chi-squared tests

-- R --

rbind-method Class "SnpMatrix"
rbind2-method Class "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

-- S --

sample-long-alleles.gz Sample datasets to illustrate data input
sample-long.gz Sample datasets to illustrate data input
sample.bed Sample datasets to illustrate data input
sample.bim Sample datasets to illustrate data input
sample.fam Sample datasets to illustrate data input
sample.info Sample datasets to illustrate data input
sample.size Extract test statistics and p-values
sample.size-method Classes "GlmTests" and "GlmTestsScore"
sample.size-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
show-method Class "GlmEstimates"
show-method Classes "GlmTests" and "GlmTestsScore"
show-method Class "ImputationRules"
show-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
show-method Class "SnpMatrix"
show-method Class "XSnpMatrix"
single.snp.tests 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs)
SingleSnpTests-class Classes "SingleSnpTests" and "SingleSnpTestsScore"
SingleSnpTestsScore-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
snp.post.multiply Pre- or post-multiply a SnpMatrix object by a general matrix
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
snp.support Data for exercise in use of the snpStats package
SnpMatrix-class Class "SnpMatrix"
snps.10 Data for exercise in use of the snpStats package
snpStats SnpMatrix and XSnpMatrix classes and methods
subject.data Test data for the snpStats package
subject.support Data for exercise in use of the snpStats package
summary-method Classes "GlmTests" and "GlmTestsScore"
summary-method Class "ImputationRules"
summary-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
summary-method Class "SnpMatrix"
summary-method Class "XSnpMatrix"
support.ld Datasets to illustrate calculation of linkage disequilibrium statistics
switch.alleles Switch alleles in columns of a SnpMatrix or in test results
switch.alleles-method Classes "GlmTests" and "GlmTestsScore"
switch.alleles-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
switch.alleles-method Class "SnpMatrix"

-- T --

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

-- W --

write.plink Write files for analysis in the PLINK toolset
write.SnpMatrix Write a SnpMatrix object as a text file

-- X --

Xchromosome Test data for the snpStats package
XSnpMatrix-class Class "XSnpMatrix"
Xsnps Test data for the snpStats package
xxt X.X-transpose for a standardized SnpMatrix

-- Y --

yri.1mb Datasets to illustrate calculation of linkage disequilibrium statistics

-- misc --

[-method Class "GlmEstimates"
[-method Classes "GlmTests" and "GlmTestsScore"
[-method Class "ImputationRules"
[-method Classes "SingleSnpTests" and "SingleSnpTestsScore"
[-method Class "SnpMatrix"
[-method Class "XSnpMatrix"
[<--method Class "XSnpMatrix"