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


[Up] [Top]

Documentation for package ‘Haplin’ version 7.0.0

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
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
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
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
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.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
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