| snpMatrix-package {snpMatrix} | R Documentation |
Implements classes and methods for large-scale SNP association studies
| Package: | snpMatrix |
| Version: | 1.5.6 |
| Date: | 2008-10-09 |
| 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 |
| Packaged: | Wed Oct 15 10:55:50 BST 2008 |
| Built: | R 2.7.1; x86_64-redhat-linux-gnu; 2008-10-15 10:53:33; 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.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 (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 regression-based 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 (source, pdf) |
snpMatrix-vignette | snpMatrix (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>