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

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Documentation for package ‘Haplin’ version 7.3.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

cbindFiles	Combine a sequence of files by columns
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
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.
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