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snpMatrix (version 1.19.24)
The snp.matrix and X.snp.matrix classes
Description
Implements classes and methods for large-scale SNP association studies
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Version
Version
1.19.24
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Version
1.19.24
License
GPL-3
Maintainer
David Clayton
Last Published
January 19th, 2015
Functions in snpMatrix (1.19.24)
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X.snp-class
Class "X.snp"
ld.snp
Function to calculate pairwise D', $r^2$
qq.chisq
Quantile-quantile plot for chi-squared tests
epsout.ld.snp
Function to write an eps file directly to visualize LD
glm.test.control
Set up control object for GLM tests
pair.result.ld.snp
Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs
read.pedfile.map
function to read the accompanying map file of a LINKAGE ped file
read.snps.pedfile
Read genotype data from a LINKAGE "pedfile"
read.pedfile.info
function to read the accompanying info file of a LINKAGE ped file
read.snps.chiamo
Read genotype data from the output of Chiamo
row.summary
Summarize rows of a snp matrix
read.wtccc.signals
read normalized signals in the WTCCC signal file format
snp.rhs.tests
Score tests with SNP genotypes as independent variable
wtccc.sample.list
read the sample list from the header of the WTCCC signal file format
xxt
X.X-transpose for a normalised snp.matrix
read.HapMap.data
function to import HapMap genotype data as snp.matrix
snp.dprime-class
Class "snp.dprime" for Results of LD calculation
ibsCount
Count alleles identical by state
single.snp.tests
1-df and 2-df tests for genetic associations with SNPs
snp.pre
Pre- or post-multiply a snp.matrix object by a general matrix
snpMatrix-package
The snp.matrix and X.snp.matrix classes
testdata
Test data for the snpMatrix package
snp.lhs.tests
Score tests with SNP genotypes as dependent variable
snp-class
Class "snp"
snp.matrix-class
Class "snp.matrix"
ibs.stats
function to calculate the identity-by-state stats of a group of samples
read.snps.long
Read SNP data in long format
for.exercise
Data for exercise in use of the snpMatrix package
ld.with
function to calculate the LD measures of specific SNPs against other SNPs
snpMatrix-internal
snpMatrix-internal
write.snp.matrix
Write a snp.matrix object as a text file
ibsDist
Distance matrix based on identity by state (IBS)
snp.cbind
Bind together two or more snp.matrix objects
plot.snp.dprime
Function to draw the pairwise D' in a eps file
X.snp.matrix-class
Class "X.snp.matrix"
read.snps.long.old
Read SNP input data in "long" format (old version)
snp.cor
Correlations with columns of a snp.matrix