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


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Documentation for package ‘Haplin’ version 6.2.0

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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
gxe Test for gene-environment interaction
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
haplinStrat Fit 'haplin' to each subset/stratum of data, determined by the argument 'strata'
haplinTDT Transmission disequilibrium tests for case-parent triad data
hapPower Power simulation for association analyses with Haplin
hapPowerAsymp Asymptotic power calculations for genetic association analyses with Haplin
hapRun Simulates genetic data and runs Haplin for each simulation
hapSim Simulation of genetic data in Haplin format
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