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


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Documentation for package ‘Haplin’ version 5.5

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
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