The snp.matrix and X.snp.matrix classes


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Documentation for package ‘chopsticks’ version 1.16.0

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A C D E F G H I L M N P Q R S T W X misc

chopsticks-package The snp.matrix and X.snp.matrix classes

-- A --

Asnps Test data for the chopsticks package
Autosomes Test data for the chopsticks package

-- C --

cbind Bind together two or more snp.matrix objects
cbind-method Class "snp.matrix"
cbind2 Bind together two or more snp.matrix objects
cbind2-method Class "snp.matrix"
chi.squared Extract test statistics and p-values
chi.squared-method Classes "snp.tests.glm" and "snp.tests.glm.score"
chi.squared-method Classes "snp.tests.single" and "snp.tests.single.score"
chopsticks The snp.matrix and X.snp.matrix classes
coerce-method Class "X.snp"
coerce-method Class "X.snp.matrix"
coerce-method Class "snp"
coerce-method Class "snp.matrix"
coerce-method Classes "snp.tests.single" and "snp.tests.single.score"
col.summary Summarize rows or columns of a snp matrix

-- D --

deg.freedom Extract test statistics and p-values
deg.freedom-method Classes "snp.tests.glm" and "snp.tests.glm.score"

-- E --

effect.sign Extract test statistics and p-values
effect.sign-method Classes "snp.tests.glm" and "snp.tests.glm.score"
effect.sign-method Classes "snp.tests.single" and "snp.tests.single.score"
effective.sample.size Extract test statistics and p-values
effective.sample.size-method Classes "snp.tests.single" and "snp.tests.single.score"
epsout.ld.snp Function to write an eps file directly to visualize LD
example-new An example of intensity data for SNP genotyping

-- F --

families Test data for family association tests
filter.rules Filter a set of imputation rules
for.exercise Data for exercise in use of the chopsticks package
Fst Calculate fixation indices

-- G --

genotype-class chopsticks-internal
genotypes Test data for family association tests
Genotypes.GenTrain1 function to do compare two snp.matrix class object
Genotypes.GenTrain2 function to do compare two snp.matrix class object
GenTrain1 function to do compare two snp.matrix class object
GenTrain2 function to do compare two snp.matrix class object
glm.test.control Set up control object for GLM tests

-- H --

haplotype-class chopsticks-internal

-- I --

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 statistics from imputation rules
imputation.nsnp Extract statistics from imputation rules
imputation.r2 Extract statistics from imputation rules
impute.snps Impute snps
initialize-method Class "X.snp.matrix"
initialize-method Class "snp.matrix"
is.na-method Class "snp.matrix"

-- L --

ld.snp Function to calculate pairwise D', r-squared
ld.with function to calculate the LD measures of specific SNPs against other SNPs
ld.with-method function to calculate the LD measures of specific SNPs against other SNPs

-- M --

misinherits Find non-Mendelian inheritances in family data

-- N --

names-method Classes "snp.tests.glm" and "snp.tests.glm.score"
names-method Classes "snp.tests.single" and "snp.tests.single.score"
niceprint Class "snp.dprime" for Results of LD calculation

-- P --

p.value Extract test statistics and p-values
p.value-method Classes "snp.tests.glm" and "snp.tests.glm.score"
p.value-method Classes "snp.tests.single" and "snp.tests.single.score"
pair.result.ld.snp Function to calculate the pairwise D', r-squared, LOD of a pair of specified SNPs
pedfile Test data for family association tests
plot-method Class "snp.reg.imputation"
plot.snp.dprime Function to draw the pairwise D' in a eps file
plotUncertainty Plot posterior probabilities of genotype assignment
pool Pool test results from several studies or sub-studies
pool2 Pool results of tests from two independent datasets
pool2-method Classes "snp.tests.glm" and "snp.tests.glm.score"
pool2-method Classes "snp.tests.single" and "snp.tests.single.score"
print.snp.dprime Class "snp.dprime" for Results of LD calculation

-- Q --

qq.chisq Quantile-quantile plot for chi-squared tests

-- R --

rbind Bind together two or more snp.matrix objects
rbind-method Class "snp.matrix"
rbind2 Bind together two or more snp.matrix objects
rbind2-method Class "snp.matrix"
read.beagle Read genotypes imputed by the BEAGLE program
read.HapMap.data function to import HapMap genotype data as snp.matrix
read.impute Read genotypes imputed by the IMPUTE2 program
read.mach Read genotypes imputed by the MACH program
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

-- S --

sample.size Extract test statistics and p-values
sample.size-method Classes "snp.tests.glm" and "snp.tests.glm.score"
sample.size-method Classes "snp.tests.single" and "snp.tests.single.score"
show-method Class "X.snp"
show-method Class "X.snp.matrix"
show-method Class "snp"
show-method Class "snp.estimates.glm"
show-method Class "snp.matrix"
show-method Class "snp.reg.imputation"
show-method Classes "snp.tests.glm" and "snp.tests.glm.score"
show-method Classes "snp.tests.single" and "snp.tests.single.score"
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.clust.plot function to do colorized cluster plots
snp.compare function to do compare two snp.matrix class object
snp.cor Correlations with columns of a snp.matrix
snp.dprime-class Class "snp.dprime" for Results of LD calculation
snp.estimates.glm-class Class "snp.estimates.glm"
snp.imputation Calculate imputation rules
snp.lhs.estimates Logistic regression with SNP genotypes as dependent variable
snp.lhs.tests Score tests with SNP genotypes as dependent variable
snp.matrix-class Class "snp.matrix"
snp.post.multiply Pre- or post-multiply a snp.matrix object by a general matrix
snp.pre.multiply Pre- or post-multiply a snp.matrix object by a general matrix
snp.rbind Bind together two or more snp.matrix objects
snp.reg.imputation-class Class "snp.reg.imputation"
snp.rhs.estimates Fit GLMs with SNP genotypes as independent variable(s)
snp.rhs.tests Score tests with SNP genotypes as independent variable
snp.support Data for exercise in use of the chopsticks package
snp.tests.glm-class Classes "snp.tests.glm" and "snp.tests.glm.score"
snp.tests.glm.score-class Classes "snp.tests.glm" and "snp.tests.glm.score"
snp.tests.single-class Classes "snp.tests.single" and "snp.tests.single.score"
snp.tests.single.score-class Classes "snp.tests.single" and "snp.tests.single.score"
snps.10 Data for exercise in use of the chopsticks package
subject.data Test data for the chopsticks package
subject.support Data for exercise in use of the chopsticks package
summary-method Class "X.snp.matrix"
summary-method Class "snp.matrix"
summary-method Class "snp.reg.imputation"
summary-method Classes "snp.tests.glm" and "snp.tests.glm.score"
summary-method Classes "snp.tests.single" and "snp.tests.single.score"
switch.alleles Switch alleles in columns of a snp.matrix or in test results
switch.alleles-method Class "snp.matrix"
switch.alleles-method Classes "snp.tests.glm" and "snp.tests.glm.score"
switch.alleles-method Classes "snp.tests.single" and "snp.tests.single.score"

-- T --

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 chopsticks package

-- W --

write.plink Write files for analysis in the PLINK toolset
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

-- X --

X.snp-class Class "X.snp"
X.snp.matrix-class Class "X.snp.matrix"
Xchromosome Test data for the chopsticks package
Xsnps Test data for the chopsticks package
xxt X.X-transpose for a standardized snp.matrix

-- misc --

[-method Class "X.snp.matrix"
[-method Class "snp.estimates.glm"
[-method Class "snp.matrix"
[-method Class "snp.reg.imputation"
[-method Classes "snp.tests.glm" and "snp.tests.glm.score"
[-method Classes "snp.tests.single" and "snp.tests.single.score"
[<--method Class "X.snp.matrix"