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 |
Asnps | Test data for the snpStats package |
Autosomes | Test data for the snpStats package |
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 |
deg.freedom | Extract test statistics and p-values |
deg.freedom-method | Classes "GlmTests" and "GlmTestsScore" |
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 |
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 |
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" |
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" |
ld | Pairwise linkage disequilibrium measures |
ld.example | Datasets to illustrate calculation of linkage disequilibrium statistics |
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 |
names-method | Classes "GlmTests" and "GlmTestsScore" |
names-method | Classes "SingleSnpTests" and "SingleSnpTestsScore" |
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 |
qq.chisq | Quantile-quantile plot for chi-squared tests |
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 |
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" |
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.SnpMatrix | Write a SnpMatrix object as a text file |
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 |
yri.1mb | Datasets to illustrate calculation of linkage disequilibrium statistics |
[-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" |