A C D E F G H I L M N P Q R S T W X misc
chopsticks-package | The snp.matrix and X.snp.matrix classes |
Asnps | Test data for the chopsticks package |
Autosomes | Test data for the chopsticks package |
cbind | Bind together two or more snp.matrix objects |
cbind-method | Class "snp.matrix" |
cbind2 | Bind together two or more snp.matrix objects |
cbind2-method | Class "snp.matrix" |
chi.squared | Extract test statistics and p-values |
chi.squared-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
chi.squared-method | Classes "snp.tests.single" and "snp.tests.single.score" |
chopsticks | The snp.matrix and X.snp.matrix classes |
coerce-method | Class "X.snp" |
coerce-method | Class "X.snp.matrix" |
coerce-method | Class "snp" |
coerce-method | Class "snp.matrix" |
coerce-method | Classes "snp.tests.single" and "snp.tests.single.score" |
col.summary | Summarize rows or columns of a snp matrix |
deg.freedom | Extract test statistics and p-values |
deg.freedom-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
effect.sign | Extract test statistics and p-values |
effect.sign-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
effect.sign-method | Classes "snp.tests.single" and "snp.tests.single.score" |
effective.sample.size | Extract test statistics and p-values |
effective.sample.size-method | Classes "snp.tests.single" and "snp.tests.single.score" |
epsout.ld.snp | Function to write an eps file directly to visualize LD |
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 chopsticks package |
Fst | Calculate fixation indices |
genotype-class | chopsticks-internal |
genotypes | Test data for family association tests |
Genotypes.GenTrain1 | function to do compare two snp.matrix class object |
Genotypes.GenTrain2 | function to do compare two snp.matrix class object |
GenTrain1 | function to do compare two snp.matrix class object |
GenTrain2 | function to do compare two snp.matrix class object |
glm.test.control | Set up control object for GLM tests |
haplotype-class | chopsticks-internal |
ibs.stats | function to calculate the identity-by-state stats of a group of samples |
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 |
impute.snps | Impute snps |
initialize-method | Class "X.snp.matrix" |
initialize-method | Class "snp.matrix" |
is.na-method | Class "snp.matrix" |
ld.snp | Function to calculate pairwise D', r-squared |
ld.with | function to calculate the LD measures of specific SNPs against other SNPs |
ld.with-method | function to calculate the LD measures of specific SNPs against other SNPs |
misinherits | Find non-Mendelian inheritances in family data |
names-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
names-method | Classes "snp.tests.single" and "snp.tests.single.score" |
niceprint | Class "snp.dprime" for Results of LD calculation |
p.value | Extract test statistics and p-values |
p.value-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
p.value-method | Classes "snp.tests.single" and "snp.tests.single.score" |
pair.result.ld.snp | Function to calculate the pairwise D', r-squared, LOD of a pair of specified SNPs |
pedfile | Test data for family association tests |
plot-method | Class "snp.reg.imputation" |
plot.snp.dprime | Function to draw the pairwise D' in a eps file |
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 "snp.tests.glm" and "snp.tests.glm.score" |
pool2-method | Classes "snp.tests.single" and "snp.tests.single.score" |
print.snp.dprime | Class "snp.dprime" for Results of LD calculation |
qq.chisq | Quantile-quantile plot for chi-squared tests |
rbind | Bind together two or more snp.matrix objects |
rbind-method | Class "snp.matrix" |
rbind2 | Bind together two or more snp.matrix objects |
rbind2-method | Class "snp.matrix" |
read.beagle | Read genotypes imputed by the BEAGLE program |
read.HapMap.data | function to import HapMap genotype data as snp.matrix |
read.impute | Read genotypes imputed by the IMPUTE2 program |
read.mach | Read genotypes imputed by the MACH program |
read.pedfile.info | function to read the accompanying info file of a LINKAGE ped file |
read.pedfile.map | function to read the accompanying map file of a LINKAGE ped file |
read.plink | Read a PLINK binary data file as a snp.matrix |
read.snps.chiamo | Read genotype data from the output of Chiamo |
read.snps.long | Read SNP data in long format |
read.snps.pedfile | Read genotype data from a LINKAGE "pedfile" |
read.wtccc.signals | read normalized signals in the WTCCC signal file format |
row.summary | Summarize rows or columns of a snp matrix |
sample.size | Extract test statistics and p-values |
sample.size-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
sample.size-method | Classes "snp.tests.single" and "snp.tests.single.score" |
show-method | Class "X.snp" |
show-method | Class "X.snp.matrix" |
show-method | Class "snp" |
show-method | Class "snp.estimates.glm" |
show-method | Class "snp.matrix" |
show-method | Class "snp.reg.imputation" |
show-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
show-method | Classes "snp.tests.single" and "snp.tests.single.score" |
single.snp.tests | 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) |
snp-class | Class "snp" |
snp.cbind | Bind together two or more snp.matrix objects |
snp.clust.plot | function to do colorized cluster plots |
snp.compare | function to do compare two snp.matrix class object |
snp.cor | Correlations with columns of a snp.matrix |
snp.dprime-class | Class "snp.dprime" for Results of LD calculation |
snp.estimates.glm-class | Class "snp.estimates.glm" |
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.matrix-class | Class "snp.matrix" |
snp.post.multiply | Pre- or post-multiply a snp.matrix object by a general matrix |
snp.pre.multiply | Pre- or post-multiply a snp.matrix object by a general matrix |
snp.rbind | Bind together two or more snp.matrix objects |
snp.reg.imputation-class | Class "snp.reg.imputation" |
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 chopsticks package |
snp.tests.glm-class | Classes "snp.tests.glm" and "snp.tests.glm.score" |
snp.tests.glm.score-class | Classes "snp.tests.glm" and "snp.tests.glm.score" |
snp.tests.single-class | Classes "snp.tests.single" and "snp.tests.single.score" |
snp.tests.single.score-class | Classes "snp.tests.single" and "snp.tests.single.score" |
snps.10 | Data for exercise in use of the chopsticks package |
subject.data | Test data for the chopsticks package |
subject.support | Data for exercise in use of the chopsticks package |
summary-method | Class "X.snp.matrix" |
summary-method | Class "snp.matrix" |
summary-method | Class "snp.reg.imputation" |
summary-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
summary-method | Classes "snp.tests.single" and "snp.tests.single.score" |
switch.alleles | Switch alleles in columns of a snp.matrix or in test results |
switch.alleles-method | Class "snp.matrix" |
switch.alleles-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
switch.alleles-method | Classes "snp.tests.single" and "snp.tests.single.score" |
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 chopsticks package |
write.plink | Write files for analysis in the PLINK toolset |
write.snp.matrix | Write a snp.matrix object as a text file |
wtccc.sample.list | read the sample list from the header of the WTCCC signal file format |
X.snp-class | Class "X.snp" |
X.snp.matrix-class | Class "X.snp.matrix" |
Xchromosome | Test data for the chopsticks package |
Xsnps | Test data for the chopsticks package |
xxt | X.X-transpose for a standardized snp.matrix |
[-method | Class "X.snp.matrix" |
[-method | Class "snp.estimates.glm" |
[-method | Class "snp.matrix" |
[-method | Class "snp.reg.imputation" |
[-method | Classes "snp.tests.glm" and "snp.tests.glm.score" |
[-method | Classes "snp.tests.single" and "snp.tests.single.score" |
[<--method | Class "X.snp.matrix" |