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Reference index for {Haplin}

Function/ClassDescription
convertPed {Haplin}Convert large ped files by creating unique IDs, converting allele coding and extracting a selection of SNPs
gwaaToHaplin {Haplin}Convert a loaded GenABEL gwaa.data object to a Haplin format character matrix
haplin {Haplin}Fitting log-linear models to case-parent triad and/or case-control data
haplinSlide {Haplin}Fit haplin in a series of sliding windows over a sequence of markers/SNPs
haplinTDT {Haplin}Transmission disequilibrium tests for case-parent triad data
haptable {Haplin}Create haplin table
lineByLine {Haplin}Line-by-line modification of files
output {Haplin}Save files with summary, table, and plot from a haplin object.
pedToHaplin {Haplin}Convert from ped format data to Haplin format
plot.haplin {Haplin}Plot a haplin object
plot.haplinTDT {Haplin}Plot a haplinTDT object
plot.haptable {Haplin}Plot a haptable object
pQQ {Haplin}QQ-plot with confidence intervals for a vector of p-values
prepPed {Haplin}Extract family and phenotype information from a ped-format file, to prepare for use in Haplin
print.haplin {Haplin}Print a haplin object
print.summary.haplin {Haplin}Print the summary of a haplin object
snpPos {Haplin}Find the column numbers of SNP identifiers/SNP numbers in a ped file
suest {Haplin}Compute a joint p-value for a list of haplin fits (usually from a sliding window approach), correcting for multiple testing.
summary.haplin {Haplin}Summary of a haplin object
summary.haplinTDT {Haplin}Summary of a haplinTDT object