| Package: |
| snpMatrix |
| Version: |
| 1.2.4 |
| Date: |
| 2008-03-17 |
| 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 indata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R qq\_chisq.R read.chiamo.R read.HapMap.R read.snps.pedfile.R single.R structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R |
| LazyLoad: |
| yes |
| biocViews: |
| Microarray, SNPsAndGeneticVariability |
| Packaged: |
| Mon Mar 17 11:46:30 2008; david |
| Built: |
| R 2.7.0; i686-pc-linux-gnu; 2008-03-17 11:47:01; unix |
Index:
X.snp-class Class "X.snp"
X.snp.matrix-class Class "X.snp.matrix"
epsout.ld.snp Function to write an eps file directly to
visualize LD
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)
ld.snp Function to calculate pairwise D', $r^2$
ld.with function to calculate the LD measures of
specific SNPs against other SNPs
pair.result.ld.snp Function to calculate the pairwise D', $r^2$,
LOD of a pair of specified SNPs
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 file
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-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.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.rhs.tests Score tests with SNP genotypes as independent
variable
snpMatrix-package The snp.matrix and X.snp.matrix classes
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 normalised snp.matrix
Further information is available in the following vignettes:
snpMatrix-vignette |
| snpMatrix (source, pdf) |