# S4 Tools for Reading and Organizing Genetic Data

## Documentation for package ‘SNPkit’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## 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