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,ANY-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: chi.squared
Aliases: chi.squared deg.freedom effect.sign p.value sample.size effective.sample.size
Keywords: utilities
Description: Extract test statistics and p-values
URL: ../../../library/snpMatrix/html/chi.squared.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: families
Aliases: families genotypes pedfile
Keywords: datasets
Description: Test data for family association tests
URL: ../../../library/snpMatrix/html/families.html

Entry: filter.rules
Aliases: filter.rules
Keywords: models regression
Description: Filter a set of imputation rules
URL: ../../../library/snpMatrix/html/filter.rules.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: imputation.maf
Aliases: imputation.maf imputation.r2
Keywords: manip
Description: Extract MAF and R-squared values from imputation rules
URL: ../../../library/snpMatrix/html/imputation.maf.html

Entry: impute.snps
Aliases: impute.snps
Keywords: models regression
Description: Impute snps
URL: ../../../library/snpMatrix/html/impute.snps.html

Entry: ld.snp
Aliases: ld.snp
Keywords: dplot htest models
Description: Function to calculate pairwise D', r-squared
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: misinherits
Aliases: misinherits
Keywords: manip
Description: Find non-Mendelian inheritances in family data
URL: ../../../library/snpMatrix/html/misinherits.html

Entry: pair.result.ld.snp
Aliases: pair.result.ld.snp
Keywords: htest models dplot
Description: Function to calculate the pairwise D', r-squared, 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: pool
Aliases: pool
Keywords: htest
Description: Pool test results from several studies or sub-studies
URL: ../../../library/snpMatrix/html/pool.html

Entry: pool2
Aliases: pool2
Keywords: htest
Description: Pool results of tests from two independent datasets
URL: ../../../library/snpMatrix/html/pool2.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.pedfile.map
Aliases: read.pedfile.map
Keywords: manip IO file
Description: function to read the accompanying map file of a LINKAGE ped file
URL: ../../../library/snpMatrix/html/read.pedfile.map.html

Entry: read.plink
Aliases: read.plink
Keywords: manip IO file utilities
Description: Read a PLINK binary data file as a snp.matrix
URL: ../../../library/snpMatrix/html/read.plink.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.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 col.summary
Keywords: utilities
Description: Summarize rows or columns 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 (or imputed 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.imputation
Aliases: snp.imputation
Keywords: models regression
Description: Calculate imputation rules
URL: ../../../library/snpMatrix/html/snp.imputation.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 [,snp.matrix,ANY,ANY,ANY-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 switch.alleles,snp.matrix,ANY-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.reg.imputation-class
Aliases: snp.reg.imputation-class show,snp.reg.imputation-method summary,snp.reg.imputation-method plot,snp.reg.imputation,missing-method [,snp.reg.imputation,ANY,missing,missing-method
Keywords: classes
Description: Class "snp.reg.imputation"
URL: ../../../library/snpMatrix/html/snp.reg.imputation-class.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: snp.tests.glm-class
Aliases: snp.tests.glm-class [,snp.tests.glm,ANY,missing,missing-method chi.squared,snp.tests.glm,missing-method deg.freedom,snp.tests.glm-method effect.sign,snp.tests.glm,logical-method names,snp.tests.glm-method p.value,snp.tests.glm,missing-method sample.size,snp.tests.glm-method show,snp.tests.glm-method summary,snp.tests.glm-method snp.tests.glm.score-class [,snp.tests.glm.score,ANY,missing,missing-method pool2,snp.tests.glm.score,snp.tests.glm.score,logical-method switch.alleles,snp.tests.glm.score,character-method
Keywords: classes
Description: Classes "snp.tests.glm" and "snp.tests.glm.score"
URL: ../../../library/snpMatrix/html/snp.tests.glm-class.html

Entry: snp.tests.single-class
Aliases: snp.tests.single-class [,snp.tests.single,ANY,missing,missing-method chi.squared,snp.tests.single,numeric-method names,snp.tests.single-method p.value,snp.tests.single,numeric-method sample.size,snp.tests.single-method effective.sample.size,snp.tests.single-method show,snp.tests.single-method summary,snp.tests.single-method snp.tests.single.score-class [,snp.tests.single.score,ANY,missing,missing-method effect.sign,snp.tests.single.score,missing-method pool2,snp.tests.single.score,snp.tests.single.score,logical-method switch.alleles,snp.tests.single.score,ANY-method
Keywords: classes
Description: Classes "snp.tests.single" and "snp.tests.single.score"
URL: ../../../library/snpMatrix/html/snp.tests.single-class.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: switch.alleles
Aliases: switch.alleles
Keywords: utilities
Description: Switch alleles in columns of a snp.matrix or in test results
URL: ../../../library/snpMatrix/html/switch.alleles.html

Entry: tdt.snp
Aliases: tdt.snp
Keywords: htest
Description: 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) in family data
URL: ../../../library/snpMatrix/html/tdt.snp.html

Entry: test.allele.switch
Aliases: test.allele.switch
Keywords: utilities
Description: Test for switch of alleles between two collections
URL: ../../../library/snpMatrix/html/test.allele.switch.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 standardized snp.matrix
URL: ../../../library/snpMatrix/html/xxt.html
