Man pages for chopsticks
The 'snp.matrix' and 'X.snp.matrix' Classes

epsout.ld.snpFunction to write an eps file directly to visualize LD
for.exerciseData for exercise in use of the snpMatrix package
glm.test.controlSet up control object for GLM tests
ibsCountCount alleles identical by state
ibsDistDistance matrix based on identity by state (IBS)
ibs.statsfunction to calculate the identity-by-state stats of a group...
ld.snpFunction to calculate pairwise D', $r^2$
ld.withfunction to calculate the LD measures of specific SNPs...
pair.result.ld.snpFunction to calculate the pairwise D', $r^2$, LOD of a pair...
plot.snp.dprimeFunction to draw the pairwise D' in a eps file
qq.chisqQuantile-quantile plot for chi-squared tests
read.HapMap.datafunction to import HapMap genotype data as snp.matrix
read.pedfile.infofunction to read the accompanying info file of a LINKAGE ped...
read.pedfile.mapfunction to read the accompanying map file of a LINKAGE ped...
read.snps.chiamoRead genotype data from the output of Chiamo
read.snps.longRead SNP data in long format
read.snps.long.oldRead SNP input data in "long" format (old version)
read.snps.pedfileRead genotype data from a LINKAGE "pedfile"
read.wtccc.signalsread normalized signals in the WTCCC signal file format
row.summarySummarize rows of a snp matrix
single.snp.tests1-df and 2-df tests for genetic associations with SNPs
snp.cbindBind together two or more snp.matrix objects
snp-classClass "snp"
snp.corCorrelations with columns of a snp.matrix
snp.dprime-classClass "snp.dprime" for Results of LD calculation
snp.lhs.testsScore tests with SNP genotypes as dependent variable
snp.matrix-classClass "snp.matrix"
snpMatrix-packageThe snp.matrix and X.snp.matrix classes
snp.prePre- or post-multiply a snp.matrix object by a general matrix
snp.rhs.testsScore tests with SNP genotypes as independent variable
testdataTest data for the snpMatrix package
write.snp.matrixWrite a snp.matrix object as a text file
wtccc.sample.listread the sample list from the header of the WTCCC signal file...
X.snp-classClass "X.snp"
X.snp.matrix-classClass "X.snp.matrix"
xxtX.X-transpose for a normalised snp.matrix
chopsticks documentation built on April 29, 2020, 5:24 a.m.