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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" |