| snpMatrix-package {snpMatrix} | R Documentation |
Implements classes and methods for large-scale SNP association studies
| Package: | snpMatrix |
| Version: | 1.7.8 |
| Date: | 2009-04-17 |
| Depends: | R(>= 2.3.0), survival, methods |
| Suggests: | hexbin |
| Enhances: | genetics |
| License: | GNU General Public Licence (GPLv3) |
| URL: | http://www-gene.cimr.cam.ac.uk/clayton/software/ |
| Collate: | ld.with.R ss.R contingency.table.R glm-test.R ibs.stats.R imputation.R indata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R plink.R qc.R qq-chisq.R read.chiamo.R read.HapMap.R read.snps.pedfile.R single.R tdt-single.R structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R |
| LazyLoad: | yes |
| biocViews: | Microarray, SNPsAndGeneticVariability |
| Built: | R 2.8.1; x86_64-pc-linux-gnu; 2009-04-17 09:49:40; unix |
Index:
X.snp-class Class "X.snp"
X.snp.matrix-class Class "X.snp.matrix"
chi.squared Extract test statistics and p-values
epsout.ld.snp Function to write an eps file directly to
visualize LD
families Test data for family association tests
filter.rules Filter a set of imputation rules
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
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)
imputation.maf Extract MAF and R-squared values from
imputation rules
impute.snps Impute snps
ld.snp Function to calculate pairwise D', r-squared
ld.with function to calculate the LD measures of
specific SNPs against other SNPs
misinherits Find non-Mendelian inheritances in family data
pair.result.ld.snp Function to calculate the pairwise D',
r-squared, LOD of a pair of specified SNPs
plot.snp.dprime Function to draw the pairwise D' in a eps file
pool Pool test results from several studies or
sub-studies
pool2 Pool results of tests from two independent
datasets
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 file
read.pedfile.map function to read the accompanying map file of a
LINKAGE ped file
read.plink Read a PLINK binary data file as a snp.matrix
read.snps.chiamo Read genotype data from the output of Chiamo
read.snps.long Read SNP data in long format
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 or columns of a snp matrix
single.snp.tests 1-df and 2-df tests for genetic associations
with SNPs (or imputed 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.imputation Calculate imputation rules
snp.lhs.tests Score tests with SNP genotypes as dependent
variable
snp.matrix-class Class "snp.matrix"
snp.pre Pre- or post-multiply a snp.matrix object by a
general matrix
snp.reg.imputation-class
Class "snp.reg.imputation"
snp.rhs.tests Score tests with SNP genotypes as independent
variable
snp.tests.glm-class Classes "snp.tests.glm" and
"snp.tests.glm.score"
snp.tests.single-class
Classes "snp.tests.single" and
"snp.tests.single.score"
snpMatrix-package The snp.matrix and X.snp.matrix classes
switch.alleles Switch alleles in columns of a snp.matrix or in
test results
tdt.snp 1-df and 2-df tests for genetic associations
with SNPs (or imputed SNPs) in family data
test.allele.switch Test for switch of alleles between two
collections
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
xxt X.X-transpose for a standardized snp.matrix
Further information is available in the following vignettes:
imputation-vignette | Imputation and meta-analysis (source, pdf) |
pca-vignette | Principal components analysis (source, pdf) |
snpMatrix-vignette | snpMatrix introduction (source, pdf) |
tdt-vignette | TDT tests (source, pdf) |
David Clayton <david.clayton@cimr.cam.ac.uk> and Hin-Tak Leung <htl10@users.sourceforge.net>
Maintainer: David Clayton <david.clayton@cimr.cam.ac.uk>