The 'snp.matrix' and 'X.snp.matrix' Classes


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Documentation for package ‘chopsticks’ version 1.66.0

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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"