FImputeExport-class     FImputeExport Class
FImputeRunner           Build FImputeRunner object
FImputeRunner-class     FImputeRunner Class
SNPFileConfig-class     SNPFileConfig Class
SNPImportList-class     SNPImportList Class
Subset                  Subset an SNPDataLong object
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
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
print.summary.SNPDataLong
                        Print method for SNPDataLong summary
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
run_admixture           Run ADMIXTURE analysis
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-method
                        Summary for SNPDataLong objects
