| cbind |
Bind together two or more snp.matrix objects |
| cbind,snp.matrix-method |
Class "snp.matrix" |
| cbind2 |
Bind together two or more snp.matrix objects |
| cbind2,snp.matrix,snp.matrix-method |
Class "snp.matrix" |
| chi.squared |
Extract test statistics and p-values |
| chi.squared,snp.tests.glm,missing-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| chi.squared,snp.tests.single,numeric-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| coerce,matrix,snp.matrix-method |
Class "snp.matrix" |
| coerce,snp,character-method |
Class "snp" |
| coerce,snp,genotype-method |
Class "snp" |
| coerce,snp,numeric-method |
Class "snp" |
| coerce,snp.matrix,character-method |
Class "snp.matrix" |
| coerce,snp.matrix,numeric-method |
Class "snp.matrix" |
| coerce,snp.matrix,X.snp.matrix-method |
Class "X.snp.matrix" |
| coerce,X.snp,character-method |
Class "X.snp" |
| coerce,X.snp,genotype-method |
Class "X.snp" |
| coerce,X.snp,numeric-method |
Class "X.snp" |
| coerce,X.snp.matrix,character-method |
Class "X.snp.matrix" |
| col.summary |
Summarize rows or columns of a snp matrix |
| p.value |
Extract test statistics and p-values |
| p.value,snp.tests.glm,missing-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| p.value,snp.tests.single,numeric-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,snp.reg.imputation,missing-method |
Class "snp.reg.imputation" |
| plot.snp.dprime |
Function to draw the pairwise D' in a eps file |
| pool |
Pool test results from several studies or sub-studies |
| pool2 |
Pool results of tests from two independent datasets |
| pool2,snp.tests.glm.score,snp.tests.glm.score,logical-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| pool2,snp.tests.single.score,snp.tests.single.score,logical-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| print.snp.dprime |
Class "snp.dprime" for Results of LD calculation |
| sample.size |
Extract test statistics and p-values |
| sample.size,snp.tests.glm-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| sample.size,snp.tests.single-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| show,snp-method |
Class "snp" |
| show,snp.matrix-method |
Class "snp.matrix" |
| show,snp.reg.imputation-method |
Class "snp.reg.imputation" |
| show,snp.tests.glm-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| show,snp.tests.single-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| show,X.snp-method |
Class "X.snp" |
| show,X.snp.matrix-method |
Class "X.snp.matrix" |
| 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.cor |
Correlations with columns of a snp.matrix |
| snp.dprime-class |
Class "snp.dprime" for Results of LD calculation |
| snp.imputation |
Calculate imputation rules |
| snp.lhs.tests |
Score tests with SNP genotypes as dependent variable |
| snp.matrix-class |
Class "snp.matrix" |
| snp.post |
Pre- or post-multiply a snp.matrix object by a general matrix |
| snp.pre |
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.tests |
Score tests with SNP genotypes as independent variable |
| snp.support |
Data for exercise in use of the snpMatrix 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" |
| snpMatrix |
The snp.matrix and X.snp.matrix classes |
| snps.10 |
Data for exercise in use of the snpMatrix package |
| subject.data |
Test data for the snpMatrix package |
| subject.support |
Data for exercise in use of the snpMatrix package |
| summary,snp.matrix-method |
Class "snp.matrix" |
| summary,snp.reg.imputation-method |
Class "snp.reg.imputation" |
| summary,snp.tests.glm-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| summary,snp.tests.single-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| summary,X.snp.matrix-method |
Class "X.snp.matrix" |
| switch.alleles |
Switch alleles in columns of a snp.matrix or in test results |
| switch.alleles,snp.matrix,ANY-method |
Class "snp.matrix" |
| switch.alleles,snp.tests.glm.score,character-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| switch.alleles,snp.tests.single.score,ANY-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| [,snp.matrix,ANY,ANY,ANY-method |
Class "snp.matrix" |
| [,snp.matrix-method |
Class "snp.matrix" |
| [,snp.reg.imputation,ANY,missing,missing-method |
Class "snp.reg.imputation" |
| [,snp.tests.glm,ANY,missing,missing-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| [,snp.tests.glm.score,ANY,missing,missing-method |
Classes "snp.tests.glm" and "snp.tests.glm.score" |
| [,snp.tests.single,ANY,missing,missing-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| [,snp.tests.single.score,ANY,missing,missing-method |
Classes "snp.tests.single" and "snp.tests.single.score" |
| [,X.snp.matrix,ANY,ANY,ANY-method |
Class "X.snp.matrix" |
| [,X.snp.matrix-method |
Class "X.snp.matrix" |
| [<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method |
Class "X.snp.matrix" |