| 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} | Finding 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 |
