Man pages for Haplin
Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
| cbindFiles | Combine a sequence of files by columns |
| convertPed | Convert large ped files by creating unique IDs, converting... |
| f.check.unique.ids | Checking uniqueness of individuals' IDs |
| f.convert.matrix.ff | Converting Haplin-formatted matrix into the new format |
| f.create.missingness.matrix | Create family matrix of data missingness |
| f.create.snp.names | Intern function for creating column names for genotype data |
| f.extract.ff.numeric | Extract a part of an ff array (matrix) and return it as... |
| f.get.gen.data.cols | Getter for the list with genetic or environmental data |
| finishParallelRun | Closing the Rmpi cluster |
| genDataGetPart | Extracting part of genetic data. |
| genDataLoad | Loading the data previously read in and saved by... |
| genDataPreprocess | Pre-processing of the genetic data |
| genDataRead | Reading the genetic data from a file |
| getChildren | Getter for all rows with children data |
| getDyads | Getter only for all dyads (child and one parent) |
| getFathers | Getter for all rows with fathers' data |
| getFullTriads | Getter for all full triads |
| getMothers | Getter for all rows with mothers' data |
| gxe | Test for gene-environment interaction |
| haplin | Fitting log-linear models to case-parent triad and/or... |
| haplinSlide | Run haplin analysis in a series of sliding windows over a... |
| haplinStrat | Fit 'haplin' to each subset/stratum of data, determined by... |
| hapPower | Power simulation for association analyses with Haplin |
| hapPowerAsymp | Asymptotic power calculations for genetic association... |
| hapRelEff | Relative efficiency comparing different study designs in... |
| hapRun | Simulates genetic data and runs Haplin for each simulation |
| hapSim | Simulation of genetic data in Haplin format |
| haptable | Create haplin table |
| initParallelRun | Initialization of the Rmpi cluster |
| lineByLine | Line-by-line modification of files |
| nfam | Count the number of families in the data |
| nindiv | Count the number of individuals in the data |
| nsnps | Count the number of markers in the data |
| output | Save files with summary, table, and plot from a haplin... |
| pedToHaplin | Convert from ped format data to Haplin format |
| pJohnson | The Johnson distributions |
| plot.haplin | Plot a haplin object |
| plot.haplinSlide | Plotter function for haplinSlide. |
| plot.haplinStrat | Plotter function for haplinStrat results. |
| plot.haptable | Plot a haptable object |
| plotPValues | Plotting p-values for relative risks |
| pQQ | QQ-plot with confidence intervals for a vector of p-values |
| print.haplin | Print a haplin object |
| print.summary.haplin | Print the summary of a haplin object |
| rbindFiles | Combine a sequence of files by rows |
| showGen | Display chosen genotypes |
| showPheno | Display phenotype part of data |
| showSNPnames | Display marker names |
| snpPos | Find the column numbers of SNP identifiers/SNP numbers in a... |
| 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... |
| summary.haplin | Summary of a haplin object |
| toDataFrame | Stack dataframes from haplinSlide into a single dataframe |
