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chopsticks (version 1.36.0)

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

1.36.0

License

GPL-3

Maintainer

HinTak Leung

Last Published

February 15th, 2017

Functions in chopsticks (1.36.0)

snp.cbind

Bind together two or more snp.matrix objects
testdata

Test data for the snpMatrix package
ibsCount

Count alleles identical by state
epsout.ld.snp

Function to write an eps file directly to visualize LD
read.snps.long

Read SNP data in long format
read.snps.pedfile

Read genotype data from a LINKAGE "pedfile"
qq.chisq

Quantile-quantile plot for chi-squared tests
single.snp.tests

1-df and 2-df tests for genetic associations with SNPs
read.snps.chiamo

Read genotype data from the output of Chiamo
read.snps.long.old

Read SNP input data in "long" format (old version)
snp.matrix-class

Class "snp.matrix"
write.snp.matrix

Write a snp.matrix object as a text file
xxt

X.X-transpose for a normalised snp.matrix
wtccc.sample.list

read the sample list from the header of the WTCCC signal file format
snp.dprime-class

Class "snp.dprime" for Results of LD calculation
snp.lhs.tests

Score tests with SNP genotypes as dependent variable
snp.rhs.tests

Score tests with SNP genotypes as independent variable
glm.test.control

Set up control object for GLM tests
row.summary

Summarize rows of a snp matrix
for.exercise

Data for exercise in use of the snpMatrix package
X.snp-class

Class "X.snp"
ibsDist

Distance matrix based on identity by state (IBS)
read.pedfile.map

function to read the accompanying map file of a LINKAGE ped file
read.wtccc.signals

read normalized signals in the WTCCC signal file format
plot.snp.dprime

Function to draw the pairwise D' in a eps file
snpMatrix-internal

snpMatrix-internal
ibs.stats

function to calculate the identity-by-state stats of a group of samples
snp-class

Class "snp"
ld.with

function to calculate the LD measures of specific SNPs against other SNPs
X.snp.matrix-class

Class "X.snp.matrix"
ld.snp

Function to calculate pairwise D', $r^2$
snp.cor

Correlations with columns of a snp.matrix
snpMatrix-package

The snp.matrix and X.snp.matrix classes
pair.result.ld.snp

Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs
read.pedfile.info

function to read the accompanying info file of a LINKAGE ped file
read.HapMap.data

function to import HapMap genotype data as snp.matrix
snp.pre

Pre- or post-multiply a snp.matrix object by a general matrix