Implements classes and methods for large-scale SNP association studies
|Author||Hin-Tak Leung <email@example.com>|
|Date of publication||None|
|Maintainer||Hin-Tak Leung <firstname.lastname@example.org>|
epsout.ld.snp: Function to write an eps file directly to visualize LD
for.exercise: Data for exercise in use of the snpMatrix package
glm.test.control: Set up control object for GLM tests
ibsCount: Count alleles identical by state
ibsDist: Distance matrix based on identity by state (IBS)
ibs.stats: function to calculate the identity-by-state stats of a group...
ld.snp: Function to calculate pairwise D', $r^2$
ld.with: function to calculate the LD measures of specific SNPs...
pair.result.ld.snp: Function to calculate the pairwise D', $r^2$, LOD of a pair...
plot.snp.dprime: Function to draw the pairwise D' in a eps file
qq.chisq: Quantile-quantile plot for chi-squared tests
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...
read.pedfile.map: function to read the accompanying map file of a LINKAGE ped...
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
single.snp.tests: 1-df and 2-df tests for genetic associations with SNPs
snp.cbind: Bind together two or more snp.matrix objects
snp-class: Class "snp"
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"
snpMatrix-package: The snp.matrix and X.snp.matrix classes
snp.pre: Pre- or post-multiply a snp.matrix object by a general matrix
snp.rhs.tests: Score tests with SNP genotypes as independent variable
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...
X.snp-class: Class "X.snp"
X.snp.matrix-class: Class "X.snp.matrix"
xxt: X.X-transpose for a normalised snp.matrix