Entry: X.snp-class
Aliases: X.snp-class coerce,X.snp,character-method coerce,X.snp,numeric-method coerce,X.snp,genotype-method show,X.snp-method
Keywords: classes
Description: Class "X.snp"
URL: ../../../library/snpMatrix/html/X.snp-class.html

Entry: X.snp.matrix-class
Aliases: X.snp.matrix-class initialize,X.snp.matrix-method [,X.snp.matrix-method [<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method coerce,X.snp.matrix,character-method coerce,snp.matrix,X.snp.matrix-method show,X.snp.matrix-method summary,X.snp.matrix-method
Keywords: classes
Description: Class "X.snp.matrix"
URL: ../../../library/snpMatrix/html/X.snp.matrix-class.html

Entry: epsout.ld.snp
Aliases: epsout.ld.snp
Keywords: dplot hplot models htest
Description: Function to write an eps file directly to visualize LD
URL: ../../../library/snpMatrix/html/epsout.ld.snp.html

Entry: for.exercise
Aliases: for.exercise snps.10 snp.support subject.support
Keywords: datasets
Description: Data for exercise in use of the snpMatrix package
URL: ../../../library/snpMatrix/html/for.exercise.html

Entry: glm.test.control
Aliases: glm.test.control
Keywords: utilities
Description: Set up control object for GLM tests
URL: ../../../library/snpMatrix/html/glm.test.control.html

Entry: ibs.stats
Aliases: ibs.stats
Keywords: utilities
Description: function to calculate the identity-by-state stats of a group of samples
URL: ../../../library/snpMatrix/html/ibs.stats.html

Entry: ibsCount
Aliases: ibsCount
Keywords: cluster
Description: Count alleles identical by state
URL: ../../../library/snpMatrix/html/ibsCount.html

Entry: ibsDist
Aliases: ibsDist
Keywords: cluster
Description: Distance matrix based on identity by state (IBS)
URL: ../../../library/snpMatrix/html/ibsDist.html

Entry: ld.snp
Aliases: ld.snp
Keywords: dplot htest models
Description: Function to calculate pairwise D', $r^2$
URL: ../../../library/snpMatrix/html/ld.snp.html

Entry: ld.with
Aliases: ld.with ld.with,snp.matrix,character-method
Keywords: dplot manip models
Description: function to calculate the LD measures of specific SNPs against other SNPs
URL: ../../../library/snpMatrix/html/ld.with.html

Entry: pair.result.ld.snp
Aliases: pair.result.ld.snp
Keywords: htest models dplot
Description: Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs
URL: ../../../library/snpMatrix/html/pair.result.ld.snp.html

Entry: plot.snp.dprime
Aliases: plot.snp.dprime
Keywords: htest models models hplot
Description: Function to draw the pairwise D' in a eps file
URL: ../../../library/snpMatrix/html/plot.snp.dprime.html

Entry: qq.chisq
Aliases: qq.chisq
Keywords: hplot
Description: Quantile-quantile plot for chi-squared tests
URL: ../../../library/snpMatrix/html/qq.chisq.html

Entry: read.HapMap.data
Aliases: read.HapMap.data
Keywords: manip IO file
Description: function to import HapMap genotype data as snp.matrix
URL: ../../../library/snpMatrix/html/read.HapMap.data.html

Entry: read.pedfile.info
Aliases: read.pedfile.info
Keywords: manip IO file
Description: function to read the accompanying info file of a LINKAGE ped file
URL: ../../../library/snpMatrix/html/read.pedfile.info.html

Entry: read.snps.chiamo
Aliases: read.snps.chiamo
Keywords: IO file
Description: Read genotype data from the output of Chiamo
URL: ../../../library/snpMatrix/html/read.snps.chiamo.html

Entry: read.snps.long
Aliases: read.snps.long
Keywords: manip IO file utilities
Description: Read SNP data in long format
URL: ../../../library/snpMatrix/html/read.snps.long.html

Entry: read.snps.long.old
Aliases: read.snps.long.old
Keywords: manip IO file utilities
Description: Read SNP input data in "long" format (old version)
URL: ../../../library/snpMatrix/html/read.snps.long.old.html

Entry: read.snps.pedfile
Aliases: read.snps.pedfile
Keywords: IO file
Description: Read genotype data from a LINKAGE "pedfile"
URL: ../../../library/snpMatrix/html/read.snps.pedfile.html

Entry: read.wtccc.signals
Aliases: read.wtccc.signals
Keywords: IO file
Description: read normalized signals in the WTCCC signal file format
URL: ../../../library/snpMatrix/html/read.wtccc.signals.html

Entry: row.summary
Aliases: row.summary
Keywords: utilities
Description: Summarize rows of a snp matrix
URL: ../../../library/snpMatrix/html/row.summary.html

Entry: single.snp.tests
Aliases: single.snp.tests
Keywords: htest
Description: 1-df and 2-df tests for genetic associations with SNPs
URL: ../../../library/snpMatrix/html/single.snp.tests.html

Entry: snp-class
Aliases: snp-class coerce,snp,character-method coerce,snp,numeric-method coerce,snp,genotype-method show,snp-method
Keywords: classes
Description: Class "snp"
URL: ../../../library/snpMatrix/html/snp-class.html

Entry: snp.cbind
Aliases: cbind rbind snp.cbind snp.rbind cbind2 rbind2
Keywords: utilities
Description: Bind together two or more snp.matrix objects
URL: ../../../library/snpMatrix/html/snp.cbind.html

Entry: snp.cor
Aliases: snp.cor
Keywords: array multivariate
Description: Correlations with columns of a snp.matrix
URL: ../../../library/snpMatrix/html/snp.cor.html

Entry: snp.dprime-class
Aliases: snp.dprime-class print.snp.dprime niceprint
Keywords: classes
Description: Class "snp.dprime" for Results of LD calculation
URL: ../../../library/snpMatrix/html/snp.dprime-class.html

Entry: snp.lhs.tests
Aliases: snp.lhs.tests
Keywords: htest
Description: Score tests with SNP genotypes as dependent variable
URL: ../../../library/snpMatrix/html/snp.lhs.tests.html

Entry: snp.matrix-class
Aliases: snp.matrix-class initialize,snp.matrix-method [,snp.matrix-method rbind2,snp.matrix,snp.matrix-method cbind2,snp.matrix,snp.matrix-method coerce,snp.matrix,numeric-method coerce,snp.matrix,character-method coerce,matrix,snp.matrix-method is.na,snp.matrix-method cbind,snp.matrix-method rbind,snp.matrix-method show,snp.matrix-method summary,snp.matrix-method
Keywords: classes
Description: Class "snp.matrix"
URL: ../../../library/snpMatrix/html/snp.matrix-class.html

Entry: snp.pre
Aliases: snp.pre snp.post
Keywords: array multivariate
Description: Pre- or post-multiply a snp.matrix object by a general matrix
URL: ../../../library/snpMatrix/html/snp.pre.html

Entry: snp.rhs.tests
Aliases: snp.rhs.tests
Keywords: htest
Description: Score tests with SNP genotypes as independent variable
URL: ../../../library/snpMatrix/html/snp.rhs.tests.html

Entry: snpMatrix-internal
Aliases: genotype-class haplotype-class
Keywords: package
Description: snpMatrix-internal
URL: ../../../library/snpMatrix/html/snpMatrix-internal.html

Entry: snpMatrix-package
Aliases: snpMatrix-package snpMatrix
Keywords: package
Description: The snp.matrix and X.snp.matrix classes
URL: ../../../library/snpMatrix/html/snpMatrix-package.html

Entry: testdata
Aliases: testdata Autosomes Xchromosome Asnps Xsnps subject.data
Keywords: datasets
Description: Test data for the snpMatrix package
URL: ../../../library/snpMatrix/html/testdata.html

Entry: write.snp.matrix
Aliases: write.snp.matrix
Keywords: manip IO file utilities
Description: Write a snp.matrix object as a text file
URL: ../../../library/snpMatrix/html/write.snp.matrix.html

Entry: wtccc.sample.list
Aliases: wtccc.sample.list
Keywords: IO file
Description: read the sample list from the header of the WTCCC signal file format
URL: ../../../library/snpMatrix/html/wtccc.sample.list.html

Entry: xxt
Aliases: xxt
Keywords: array multivariate
Description: X.X-transpose for a normalised snp.matrix
URL: ../../../library/snpMatrix/html/xxt.html
