Man pages for NikNakk/snpStats
SnpMatrix and XSnpMatrix classes and methods
| chi.squared | Extract test statistics and p-values |
| convert.snpMatrix | Convert 'snpMatrix' objects to 'snpStats' objects |
| example-new | An example of intensity data for SNP genotyping |
| families | Test data for family association tests |
| filter.rules | Filter a set of imputation rules |
| for.exercise | Data for exercise in use of the snpStats package |
| Fst | Calculate fixation indices |
| GlmEstimates-class | Class "GlmEstimates" |
| glm.test.control | Set up control object for GLM computations |
| GlmTests-class | Classes "GlmTests" and "GlmTestsScore" |
| ibsCount | Count alleles identical by state |
| ibsDist | Distance matrix based on identity by state (IBS) |
| imputation.maf | Extract statistics from imputation rules |
| ImputationRules-class | Class "ImputationRules" |
| impute.snps | Impute snps |
| ld | Pairwise linkage disequilibrium measures |
| ld.example | Datasets to illustrate calculation of linkage disequilibrium... |
| mean2g | Raw coding of posterior probabilities of SNP genotype |
| misinherits | Find non-Mendelian inheritances in family data |
| mvtests | Multivariate SNP tests |
| 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 |
| pp | Unpack posterior probabilities from one-byte codes |
| qq.chisq | Quantile-quantile plot for chi-squared tests |
| read.beagle | Read genotypes imputed by the BEAGLE program |
| read.impute | Read genotypes imputed by the IMPUTE2 program |
| read.long | Read SNP genotype data in long format |
| read.mach | Read genotypes imputed by the MACH program |
| read.pedfile | Read a pedfile as '"SnpMatrix"' object |
| read.plink | Read a PLINK binary data file as a SnpMatrix |
| read.snps.long | Read SNP data in long format (deprecated) |
| row.summary | Summarize rows or columns of a snp matrix |
| sample | Sample datasets to illustrate data input |
| single.snp.tests | 1-df and 2-df tests for genetic associations with SNPs (or... |
| SingleSnpTests-class | Classes "SingleSnpTests" and "SingleSnpTestsScore" |
| sm.compare | Compare two SnpMatrix objects |
| snp.cor | Correlations with columns of a SnpMatrix |
| 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 |
| SnpMatrix-class | Class "SnpMatrix" |
| snp.pre.multiply | Pre- or post-multiply a SnpMatrix object by a general matrix |
| snp.rhs.estimates | Fit GLMs with SNP genotypes as independent variable(s) |
| snp.rhs.tests | Score tests with SNP genotypes as independent variable |
| snpStats-package | SnpMatrix and XSnpMatrix classes and methods |
| switch.alleles | Switch alleles in columns of a SnpMatrix or in test results |
| tdt.snp | 1-df and 2-df tests for genetic associations with SNPs (or... |
| test.allele.switch | Test for switch of alleles between two collections |
| testdata | Test data for the snpStats package |
| write.plink | Write files for analysis in the PLINK toolset |
| write.snp.matrix | Write a SnpMatrix object as a text file |
| XSnpMatrix-class | Class "XSnpMatrix" |
| xxt | X.X-transpose for a standardized SnpMatrix |
