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