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" |