snpMatrix-package | The snp.matrix and X.snp.matrix classes |
Asnps | Test data for the snpMatrix package |
Autosomes | Test data for the snpMatrix 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" |
coerce-method | Class "X.snp" |
coerce-method | Class "X.snp.matrix" |
coerce-method | Class "snp" |
coerce-method | Class "snp.matrix" |
convert.snpMatrix | snpMatrix-internal |
convert.snpMatrix.dir | snpMatrix-internal |
epsout.ld.snp | Function to write an eps file directly to visualize LD |
for.exercise | Data for exercise in use of the snpMatrix package |
genotype-class | snpMatrix-internal |
glm.test.control | Set up control object for GLM tests |
haplotype-class | snpMatrix-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) |
initialize-method | Class "X.snp.matrix" |
initialize-method | Class "snp.matrix" |
is.na-method | Class "snp.matrix" |
ld.snp | Function to calculate pairwise D', $r^2$ |
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 |
niceprint | Class "snp.dprime" for Results of LD calculation |
pair.result.ld.snp | Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs |
plot.snp.dprime | Function to draw the pairwise D' in a eps file |
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.HapMap.data | function to import HapMap genotype data as snp.matrix |
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.snps.chiamo | Read genotype data from the output of Chiamo |
read.snps.long | Read SNP data in long format |
read.snps.long.old | Read SNP input data in "long" format (old version) |
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 of a snp matrix |
show-method | Class "X.snp" |
show-method | Class "X.snp.matrix" |
show-method | Class "snp" |
show-method | Class "snp.matrix" |
single.snp.tests | 1-df and 2-df tests for genetic associations with 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.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.rhs.tests | Score tests with SNP genotypes as independent variable |
snp.support | Data for exercise in use of the snpMatrix package |
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-method | Class "X.snp.matrix" |
summary-method | Class "snp.matrix" |
testdata | Test data for the snpMatrix package |
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 snpMatrix package |
Xsnps | Test data for the snpMatrix package |
xxt | X.X-transpose for a normalised snp.matrix |
[-method | Class "X.snp.matrix" |
[-method | Class "snp.matrix" |
[<--method | Class "X.snp.matrix" |