Package index • SNPtools

All functions
`FImputeExport-class`	FImputeExport Class
`FImputeRunner-class`	FImputeRunner Class
`FImputeRunner()`	Build FImputeRunner object
`SNPDataLong-class`	SNPDataLong Class
`SNPFileConfig-class`	SNPFileConfig Class
`SNPImportList-class`	SNPImportList Class
`Subset()`	Subset an SNPDataLong object
`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
`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
`ibs.pair()`	IBS pair statistics
`importAllGenos()`	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
`qcSNPs()`	Quality Control for SNPDataLong with optional criteria
`qcSamples()`	Quality control on samples
`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
`saveFImpute()`	Save genotype and map files in FImpute format
`saveFImputeRaw()`	Export genotypes and map using basic arguments
`savePlink()`	Save SNPDataLong object to PLINK format
`summary(<SNPDataLong>)`	Summary for SNPDataLong objects

Reference

All functions