The snp.matrix and X.snp.matrix classes


[Package List] [Top]

Documentation for package ‘snpMatrix’ version 1.10.3

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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

-- --

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

-- A --

Asnps Test data for the snpMatrix package
Autosomes Test data for the snpMatrix package

-- C --

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

-- D --

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

-- E --

effect.sign Extract test statistics and p-values
effect.sign,snp.tests.glm,logical-method Classes "snp.tests.glm" and "snp.tests.glm.score"
effect.sign,snp.tests.single.score,missing-method Classes "snp.tests.single" and "snp.tests.single.score"
effective.sample.size Extract test statistics and p-values
effective.sample.size,snp.tests.single-method Classes "snp.tests.single" and "snp.tests.single.score"
epsout.ld.snp Function to write an eps file directly to visualize LD

-- 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 snpMatrix package

-- G --

genotype-class snpMatrix-internal
genotypes Test data for family association tests
glm.test.control Set up control object for GLM tests

-- H --

haplotype-class snpMatrix-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,snp.matrix-method Class "snp.matrix"
initialize,X.snp.matrix-method Class "X.snp.matrix"
is.na,snp.matrix-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,snp.matrix,character-method function to calculate the LD measures of specific SNPs against other SNPs

-- M --

misinherits Find non-Mendelian inheritances in family data

-- N --

names,snp.tests.glm-method Classes "snp.tests.glm" and "snp.tests.glm.score"
names,snp.tests.single-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,snp.tests.glm,missing-method Classes "snp.tests.glm" and "snp.tests.glm.score"
p.value,snp.tests.single,numeric-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,snp.reg.imputation,missing-method Class "snp.reg.imputation"
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
pool2,snp.tests.glm.score,snp.tests.glm.score,logical-method Classes "snp.tests.glm" and "snp.tests.glm.score"
pool2,snp.tests.single.score,snp.tests.single.score,logical-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,snp.matrix-method Class "snp.matrix"
rbind2 Bind together two or more snp.matrix objects
rbind2,snp.matrix,snp.matrix-method Class "snp.matrix"
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.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,snp.tests.glm-method Classes "snp.tests.glm" and "snp.tests.glm.score"
sample.size,snp.tests.single-method Classes "snp.tests.single" and "snp.tests.single.score"
show,snp-method Class "snp"
show,snp.matrix-method Class "snp.matrix"
show,snp.reg.imputation-method Class "snp.reg.imputation"
show,snp.tests.glm-method Classes "snp.tests.glm" and "snp.tests.glm.score"
show,snp.tests.single-method Classes "snp.tests.single" and "snp.tests.single.score"
show,X.snp-method Class "X.snp"
show,X.snp.matrix-method Class "X.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 imputation rules
snp.lhs.tests Score tests with SNP genotypes as dependent variable
snp.matrix-class Class "snp.matrix"
snp.post Pre- or post-multiply a snp.matrix object by a general matrix
snp.pre 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.tests Score tests with SNP genotypes as independent variable
snp.support Data for exercise in use of the snpMatrix 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"
snpMatrix The snp.matrix and X.snp.matrix classes
snps.10 Data for exercise in use of the snpMatrix package
subject.data Test data for the snpMatrix package
subject.support Data for exercise in use of the snpMatrix package
summary,snp.matrix-method Class "snp.matrix"
summary,snp.reg.imputation-method Class "snp.reg.imputation"
summary,snp.tests.glm-method Classes "snp.tests.glm" and "snp.tests.glm.score"
summary,snp.tests.single-method Classes "snp.tests.single" and "snp.tests.single.score"
summary,X.snp.matrix-method Class "X.snp.matrix"
switch.alleles Switch alleles in columns of a snp.matrix or in test results
switch.alleles,snp.matrix,ANY-method Class "snp.matrix"
switch.alleles,snp.tests.glm.score,character-method Classes "snp.tests.glm" and "snp.tests.glm.score"
switch.alleles,snp.tests.single.score,ANY-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 snpMatrix package

-- W --

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 snpMatrix package
Xsnps Test data for the snpMatrix package
xxt X.X-transpose for a standardized snp.matrix

-- misc --

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