Man pages for stefanedwards/Siccuracy
Pipeline Package for AlphaImpute

auxfuncAuxiliary functions
cbind_snp_filesColumn bind files with genotype matrices
convert_phasesConvert phase files to genotype files.
convert_plinkConverts PLINK binary format to SNP formatted file.
convert_plinkAConvert PLINK recoded A to SNP file.
deprecatedDeprecated functions
extract.gtExtract genotypes from SNP objects.
extract.snps#' Extracts #' #' @inheritParams extract.snps #' @return...
haps-formatSHAPEIT haps/sample format
heterozygosityCalculates hetereozygosity stats for a single population
imputation_accuracyImputation accuracy, aka. correlations
mask_snp_fileMasks entries of a single SNP chip file.
oxfordOxford format
parseformatFormat descriptors
rbind_snp_filesCombines rows of two SNP chip files and provides masking.
read.snpsRead genotype matrix from file.
SiccuracyStefan's imputation accuracy package
VCF-formatVCF objects in Siccuracy
write.snpsWrite genotype matrices to file, AlphaImpute style.
stefanedwards/Siccuracy documentation built on Dec. 14, 2017, 7:41 p.m.