The 'snp.matrix' and 'X.snp.matrix' Classes
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Documentation for package ‘chopsticks’ version 1.66.0
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| snpMatrix-package | The snp.matrix and X.snp.matrix classes |
| Asnps | Test data for the snpMatrix package |
| Autosomes | Test data for the snpMatrix package |
| 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" |
| coerce-method | Class "X.snp" |
| coerce-method | Class "X.snp.matrix" |
| coerce-method | Class "snp" |
| coerce-method | Class "snp.matrix" |
| convert.snpMatrix | snpMatrix-internal |
| convert.snpMatrix.dir | snpMatrix-internal |
| epsout.ld.snp | Function to write an eps file directly to visualize LD |
| for.exercise | Data for exercise in use of the snpMatrix package |
| genotype-class | snpMatrix-internal |
| glm.test.control | Set up control object for GLM tests |
| haplotype-class | snpMatrix-internal |
| 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) |
| initialize-method | Class "X.snp.matrix" |
| initialize-method | Class "snp.matrix" |
| is.na-method | Class "snp.matrix" |
| ld.snp | Function to calculate pairwise D', $r^2$ |
| 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 |
| niceprint | Class "snp.dprime" for Results of LD calculation |
| pair.result.ld.snp | Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs |
| plot.snp.dprime | Function to draw the pairwise D' in a eps file |
| print.snp.dprime | Class "snp.dprime" for Results of LD calculation |
| qq.chisq | Quantile-quantile plot for chi-squared tests |
| 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.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.snps.chiamo | Read genotype data from the output of Chiamo |
| read.snps.long | Read SNP data in long format |
| read.snps.long.old | Read SNP input data in "long" format (old version) |
| 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 of a snp matrix |
| show-method | Class "X.snp" |
| show-method | Class "X.snp.matrix" |
| show-method | Class "snp" |
| show-method | Class "snp.matrix" |
| single.snp.tests | 1-df and 2-df tests for genetic associations with 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.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.rhs.tests | Score tests with SNP genotypes as independent variable |
| snp.support | Data for exercise in use of the snpMatrix package |
| 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-method | Class "X.snp.matrix" |
| summary-method | Class "snp.matrix" |
| testdata | Test data for the snpMatrix package |
| 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.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 normalised snp.matrix |
| [-method | Class "X.snp.matrix" |
| [-method | Class "snp.matrix" |
| [<--method | Class "X.snp.matrix" |