# Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

## Documentation for package ‘Haplin’ version 7.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
f.convert.matrix.ff | Converting Haplin-formatted matrix into the new format
f.create.snp.names | Intern function for creating column names for genotype data
finishParallelRun | Closing the Rmpi cluster
genDataGetPart | Extracting part of genetic data.
genDataLoad | Loading the data previously read in and saved by "genDataRead"
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 case-control data
haplinSlide | Run haplin analysis in a series of sliding windows over a sequence of markers/SNPs
haplinStrat | Fit 'haplin' to each subset/stratum of data, determined by the argument 'strata'
hapPower | Power simulation for association analyses with Haplin
hapPowerAsymp | Asymptotic power calculations for genetic association analyses with Haplin
hapRelEff | Relative efficiency comparing different study designs in genetic association analysis with Haplin
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
JohnsonFit | The Johnson distributions
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 object.
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 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
toDataFrame | Stack dataframes from haplinSlide into a single dataframe