S4 Tools for Reading and Organizing Genetic Data
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Documentation for package ‘SNPkit’ version 0.1.0
Help Pages
| as_snpmatrix | Convert a genotype matrix or data.frame to snpStats::SnpMatrix |
| cbind_SnpMatrix | Safe cbind for SnpMatrix preserving dimnames |
| check.call.rate | Check SNP call rate |
| check.ibs | Check Identity-By-State (IBS) for a genotype pair |
| check.identical.samples | Check identical samples based on distance |
| check.identical.samples.by.block | Check identical samples by block |
| check.mendelian.inconsistencies | Check Mendelian inconsistencies |
| check.mendelian.inconsistencies.pair | Check Mendelian inconsistencies for a pair |
| check.sample.call.rate | Check Sample Call Rate |
| check.sample.heterozygosity | Check sample heterozygosity |
| check.snp.chromo | Check SNP by chromosome |
| check.snp.hwe | Check SNP Hardy-Weinberg equilibrium deviation |
| check.snp.hwe.chi2 | Check SNPs for Hardy-Weinberg equilibrium deviation using chi-square p-values |
| check.snp.maf | Check SNP minor allele frequency |
| check.snp.mgf | Check SNP missing genotype frequencies |
| check.snp.monomorf | Check SNP monomorphic status |
| check.snp.no.position | Check SNP no position |
| check.snp.same.position | Check SNPs mapped to the same position |
| combineSNPData | Combine multiple SNPDataLong objects |
| doPCA | Do genome relationship matrix PCA |
| exploratory.plots | Exploratory plots for SNP and sample summary |
| FImputeExport-class | FImputeExport Class |
| FImputeRunner | Build FImputeRunner object |
| FImputeRunner-class | FImputeRunner Class |
| genoToDF | Convert geno slot from SNPDataLong to a data.frame |
| get.correl.fc | Get correlation (fc method) |
| get.gender | Get gender based on heterozygosity |
| get.hwe.chi2 | Get HWE chi-square p-values |
| getGeno | Flexible and efficient genotype file reading with autodetection using fread |
| getGeno-method | Flexible and efficient genotype file reading with autodetection using fread |
| ibs.pair | IBS pair statistics |
| importAllGenos | Import and combine multiple genotype configurations |
| importAllGenos-method | Import and combine multiple genotype configurations |
| importFImputeResults | Import imputed FImpute results from disk |
| import_geno_list | Import multiple genotype datasets from a list of configurations |
| pairs2sets | Convert pairs to sets |
| plotPCAgroups | Plot PCA groups from anticlustering result |
| print.summary.SNPDataLong | Print method for SNPDataLong summary |
| qcSamples | Quality control on samples |
| qcSamples-method | Quality control on samples |
| qcSNPs | Quality Control for SNPDataLong with optional criteria |
| qcSNPs-method | Quality Control for SNPDataLong with optional criteria |
| qc_header | Formatted header message |
| rbindSnpFlexible | Faster row-bind for SnpMatrix objects with differing columns |
| rbind_SnpMatrix | Safe rbind for SnpMatrix preserving dimnames |
| read.fimpute | Read imputed genotypes from FImpute output and return SNPDataLong object |
| runAnticlusteringPCA | Run PCA and anticlustering on SNPDataLong |
| runFImpute | Run FImpute from a FImputeRunner object |
| runFImpute-method | Run FImpute from a FImputeRunner object |
| run_admixture | Run ADMIXTURE analysis |
| saveFImpute | Save genotype and map files in FImpute format |
| saveFImpute-method | Save genotype and map files in FImpute format |
| saveFImputeRaw | Export genotypes and map using basic arguments |
| savePlink | Save SNPDataLong object to PLINK format |
| SNPFileConfig-class | SNPFileConfig Class |
| SNPImportList-class | SNPImportList Class |
| Subset | Subset an SNPDataLong object |
| Subset-method | Subset an SNPDataLong object |
| summary-method | Summary for SNPDataLong objects |